Date: Wed Jan 1 05:15:17 EST 2003
Name: Gad
Email:gad.yagil@weizmann.ac.il URL:http://www.weizmann.ac.il/~lcyagil Remote Host: 212.199.184.47
Subject: contact
It was a pleasure meeting you 2 I hope you enjoyed the rest of your stay.
I wonder whether this continues to be the upto date site. If there
is now another one, please let me know. I shall soon try if I can find how to run with DNA Parameters, and let you know.
I am preparing a cover with the Yeast CEN4 paper I mentioned to you,
and other papers with the purine/pyrimidine tract story, i shall be glad to have your comments.
It was nice meeting you,
Gad
Date: Sat Jan 11 09:11:31 EST 2003
Name: L.MuthuSelvi
Email:selvimallax_82@hotmail.com URL:http:// Remote Host: 210-210-32-47.lan.sify.net
Subject: structure
Respected Sir/Mam,
I wish to have the nice structure of the sequence
including all your calculations.What can I do?Kindly,provide me the possible suggestions!
Thank you.
Date: Sat Jan 25 16:10:58 EST 2003
Name: Maciej
Email: URL: Remote Host: pa157.opole.sdi.tpnet.pl
Subject: Solver
Your Pell Equation solver is great, thanks for making it.
Date: Sun Jan 26 03:46:05 EST 2003
Name: Mathew
Email:drmatz@rediffmail.com URL:http:// Remote Host: ool-18bcbc3f.dyn.optonline.net
Subject: Hi
Sir,
I have gone through all your works.I am having a knowledge of both Computers as well as Biology especially Genetic.
I would happy to work animal related research you have.I am a veterinary doctor and a Major in Computer Science( expected by May 2002).
Please do the needful to guide me in my endeavour.
Thank you
Mathew Thomas
Date: Mon Feb 3 01:42:13 EST 2003
Name: Duleep
Email:dksam@iihr.kar.nic.in URL:http:// Remote Host: iihr.kar.nic.in
Subject: Thanks
Respected Dr.Zuker, thanks for making this wonderful resource, I hope that by and by I will understand more and use better, with regards Samuel, Ind inst of Hort Research, Bangalore INDIA
Date: Fri Feb 7 14:53:35 EST 2003
Name: Tadeusz
Email:tmalin@insad.pl URL:http:// Remote Host: isk.insad.pl
Subject: Many
Dear Professor Zuker,
I would like to say many, many thanks to you and to your co-workers
for creating and maintaining this wonderful service.
My first impression is that it is really great and I shall be happy to visit it again and again. It is wonderful that there are still some people sharing their achievements in a traditional way -
obviously having the satisfaction from providing help to the others.
It is good in a world nowadays.
With best wishes
Tadeusz Malinowski
Institute of Pomology and Floriculture, Skierniewice, Poland
Date: Mon Feb 10 02:51:52 EST 2003
Name: Eitan
Email:bcbibi@wicc.weizmann.ac.il URL:http:// Remote Host: 212.199.50.186
Subject: Great
Date: Wed Feb 19 22:41:01 EST 2003
Name: Rupali
Email:ruparbhane@yahoo.com URL:http:// Remote Host: rupali
Subject: Wonderful
Dear Prof. Zuker,
Many thanks for developing such a wonderful site. This site is very useful for people working in the RNA folding.
From Beginners to Advance Learners, each one will be beneficial.
Sincerely,
Rupali.
Date: Thu Feb 20 15:49:51 EST 2003
Name: Leonid
Email:leonid_buryanovskyy@nymc.edu URL:http:// Remote Host: ns2.nymc.edu
Subject: Great site. Thanks for the very good service. Although I am quite a beginner, the program is very convenient.
Leo
Date: Fri Feb 21 07:18:08 EST 2003
Name: Sergeant
Email:alain.sergeant@ens-lyon.fr URL:http:// Remote Host: 140.77.192.33
Subject: publication
Dear Dr Zuker,
Am I allowed to include in a publication pictures of RNA folding obtained through your web si!te, and what shall I cite if allowed.
Thanks for your answer
Very sincerely,
Alain Sergeant
PhD, DR1 CNRS
M. Zuker replies:
Yes, you are allowed to use any of the images that are created for any of your foldings. I have submitted an article that is targeted for a special issue of Nucleic Acids Research that will deal with web servers. In the mean time, please cite the articles that are cited on this page.Date: Tue Mar 4 07:27:03 EST 2003
Name: Morgane
Email:morgane@get2net.dk URL:http:// Remote Host: p422-016.ppp.get2net.dk
Subject: This is one of the most helpfull sites I have come across. Thank you so much to Dr Zuker and his co-workers for creating and maintaining this resource! If I may, allow me to correct an insignificant detail: the link to the French version of this page should read "Cette page...", not "Ce page...".
Morgane Thomsen, Copenhagen.
M. Zuker replies:
Thanks for the tip. The French version is now corrected.
Date: Tue Mar 4 19:44:42 EST 2003
Name: xiaoying
Email:xiaoying.chen@roche.com URL:http:// Remote Host: p196-3-48-10.pal.roche.com
Subject: batch
Dear Dr. Zucker,
Can we submit multiple sequences in a single batch submission? or in any way?
Thanks,
--xiaoying
M. Zuker replies:
You may submit many (hundreds) of sequences in a single submission using the quikfold or zipfold servers. The quikfold server gives no graphics. The zipfold server gives only minimum free energies. Sequence size is limited and only "immediate jobs" are allowed.
URLS: quikfold serverzipfold serverDate: Fri Mar 21 03:05:15 EST 2003
Name: guanyuan
Email:guanyuan008@hotmail.com URL:http:// Remote Host: hotmail.com
Subject: It's
I'm a real freshman in this domain, and I found this is a real wonderful web for studying RNA. But I still don't Kown the meaning of some of the information in Thermal details.
Date: Fri Mar 21 09:38:23 EST 2003
Name: Arnold
Email:sciarnold@yahoo.com URL:http:// Remote Host: upchdat.upch.edu.pe
Subject: Complaint
Dear Professor Michael Zuker,
I have used your server to calculate the Tm of the secundary structure of my predicted PCR product about a week a go. Today, March 21st, I made a check of these values and I found that most of them have changed. Some of them in about 6 degrees, that is really important for the experiment I shall carry. Why does that happens?.
Another issue is that I don't understand the reason to ask for a folding temperature when one just wants to know the Tm of a oligonucleotide sequence.
Yours faithfully.
-Arnold Pérez Goicochea
Date: Thu Mar 27 03:50:50 EST 2003
Name: Markus
Email:Markus.Boehl@chemie.tu-dresden.de URL:http:// Remote Host: cbcp49.chm.tu-dresden.de
Subject: What's
Dear Mr. Zuker....
....mfold is really a great tool for our needs, we use it intensively, but I was looking for one information I was not able to find on the hole mfold page. What is the dimension of your energy calculation?? Is it kJ/mol or Kcal/mol???
Thanks for the possibilty to use mfold....and best wishes from Dresden
Markus Boehl
M. Zuker replies:
The units are, and have always been, kcal/mol (not Kcal).
Date: Sat Mar 29 12:49:27 EST 2003
Name: kavitha
Email:kavithareddyk@yahoo.com URL:http:// Remote Host: 61.1.164.144
Subject: suggestion
i guess some detailed lecture notes on each related program would help more in understanding
Date: Wed Apr 2 07:22:09 EST 2003
Name: Email: URL:http:// Remote Host: imsb47-247.mbio.au.dk
Subject: Concerning the Hybridization Server:
It would be useful if the total nucleic acid concentration could be given in uM or pM, since it can be entered in the form. The 'problem' is that the program accepts that you write uM/pM, but then still calculates as if the concentration were given in mM or M.
-Otherwise thank you for a very usefull website!
Date: Mon Apr 7 20:19:32 EDT 2003
Name: Nicholas
Email:nmills@itsa.ucsf.edu URL: Remote Host: udp021988uds.ucsf.edu
Subject: Maximum
We are currently pursuing an idea in which we would like to fold a large number of DNA sequences in the promoter regions of different genes. Do you have any suggestions for submitting large numbers of DNA sequences? As a first pass, energy values alone would be valuable.
Thanks
Nicholas Mills
UCSF Dept. of Biochemistry
M. Zuker replies:
You may fold hundreds of DNA or RNA sequences at a time using related servers.
quikfold server
Fold many sequences at once. Optimal and suboptimal foldings are given in RNAML, ct file and ASCII file formats. No graphics. Fast.
Tm server
Predict minimum folding free energies and 2-state Tms only for many sequence at once. Faster.
zipfold server
Predict minimum folding free energies only for many sequences at once. Even faster.
Found your website to be very useful and fairly user friendly.
I learned of it through BioRAD. Would have liked to learn more
about the other variables (like what they mean).
Is the hybridization algorithm in your web also based on a minimum free energy (mfe)? Or are two strands viewed as two parts of one single-strand DNA (RNA) and just some constraints added?
M. Zuker replies:
The existing hybridization algorithm is based on minimum free energy at some (arbitrary temperature). The default temperature is 55 °C. The melting temperature, Tm, is based on a simple two-state model that assumes either complete hybridization at minimum free energy or total separation of the two strands. No intermediates are considered. Hybridization is computed for two separate strands of DNA or RNA. In initiation free energy is used to bring the two strands together.
Date: Wed Apr 23 05:58:01 EDT 2003
Name: Peter
Email:Peter.Weekers@rug.ac.be URL:http:// Remote Host: molphylo.rug.ac.be
Subject: MFOLD
Hi Mike,
Once again I had to use your magnificent MFOLD program. As before, it works wonderful. Thanks again for this very nice facility.
Cheers,
Peter
Date: Thu Apr 24 12:23:43 EDT 2003
Name: Jiong
Email:jiong.zhang@stjude.org URL:http:// Remote Host: gatekeeper.stjude.org
Subject: query
Hi, thanks for the wonderful web server. I have a large number of oligos (40-60 bases long) that I would like to look for hairpin loops. But I don't want to swamp your server. What is the limit on the number of short sequences that I can submit? Thanks.
M. Zuker replies:
There is no limit. Do your worst. I dare you. (However, if you really mess up the server, you will be blocked from the site until you moderate your requests.) If you are just looking for haipins in a (large) number of oligos, then you should be using my "quikfold" server. You can submit up to about 1000 sequences in a single run.
Date: Mon Apr 28 09:50:18 EDT 2003
Name: Stella
Email:casinos@casinos-casino.org URL: Remote Host: afontenayssb-109-1-1-173.abo.wanadoo.fr
Subject: great
Hello, i live in France, and i studied a little bit all about DNA, and also chemicals formulas. I admire your job as i know how difficult it is to analyse such human elementaries bricks. Thanks to your work, may be genetic therapy, in a futur, will be a great solution. so thanks for your studies of Acid Ribonucleic,..
Date: Fri May 2 10:21:34 EDT 2003
Name: mark
Email: URL:http:// Remote Host: bh23218.umsl.edu
Subject: at
I'm at a Univ.MO-St. Louis computer, can't complete assignment to visualize RNA folding sequence. Can't download mfold, can't display any image. Wasting too much time. Date: Sat May 3 18:20:29 EDT 2003
Name: shiri
Email:shirimazor@hotmail.com URL:http:// Remote Host: diup-13-175.inter.net.il
Subject: using
Mr. Zuker,
im only a young biology student, but manage your program and i want to thank u for creating such a usfull, easy and reliable program.
Date: Thu May 8 15:43:49 EDT 2003
Name: Allison
Email:allison@bio-alliance.com URL:http://www.bio-alliance.com Remote Host: rrcs-west-24-24-135-247.biz.rr.com
Subject: Your
Dear Dr. Zuker,
Love your Bar-Mitzvah picture.
Allison M. Zuker replies:
Thanks, except you're off by 11 years. I'm 24 years old in that picture and attending a friend's wedding.
Date: Fri May 23 18:15:12 EDT 2003
Name: David
Email:dmcohen@mail.uh.edu URL:http:// Remote Host: 129-7-197-241.dhcp.uh.edu
Subject: my
I enter the following 5 sequences in the window of the TM server:
AGGTGAACTGCAAATACATAGGGACTGATGCCTTCCACTTCCTCTGC;
TGAAGCTGAAAGACCATCTTCAGTGACACCTCCTGCAATCACAATTT;
ACACTAGCGCAGTTATCCTACACAAGGCATCTCCGATTCTCCAGTCA;
AGAGAGAAAGGGAGGGCAAGGGAGAAGGGAGAAGGGAAGAGAGAAAC;
ACTTTAAGCATTGGATCATAGGTTGTGGGTGCCATAGGAGAGGTGGG;
However, I only get information (dG, dS, dH, and Tm) on 4 of them!
Can you tell me why ? This is important to people with thousands of short sequences, such as myself.
Thanks.
David Cohen
Here is the output:
may23_#9 is the 3588719th group of nucleic acid sequences folded on the Rouillard server.
- vendredi 23 mai 2003 18:00:37 EDT / divendres 23 mai 2003 18:00:37 EDT -
Folding may23_#9 at 37° C. ()
[Na+] = 1.0 M, [Mg++] = 0.0 M, oligo correction
- Computed for 129-7-197-241.dhcp.uh.edu -
- Output -
Computed free energies
1. dG = -0.9 dH = -16.1 dS = -49.0 Tm = 55.4
2. dG = -2.9 dH = -79.3 dS = -246.3 Tm = 48.8
3. dG = -1.7 dH = -39.3 dS = -121.2 Tm = 51.0
4. dG = -0.6 dH = -29.0 dS = -91.6 Tm = 43.6
These computations were performed on cn-20.bioinfo.z in 0 min. and 0.26 sec. The results have already been erased.
M. Zuker replies:
Your third sequence has no possible folding, so results are not given for it. There is no possible secondary structure because there is no possibility to have at least one pair of consecutive base pairs. I solved this problem a while ago with the version of the server that most people hit directly using a script. I've switched over to this plain output. You'll see that missing sequences are clearly indicated because the sequence numbering will jump by more than one. Try it out and give me your opinion.
Date: Thu Jun 5 08:01:13 EDT 2003
Name: Anna
Email:mastrangelo@iscfoggia.it URL:http:// Remote Host: host202-120.pool80105.interbusiness.it
Subject: folding
I'm working on plant UTR. Is it possible to change the temperature value which is fixed at 37°C?
M. Zuker replies:
Yes, it is possible, but you must use the older RNA energy parameters. Go to RNA mfold version 2.3 server.
Date: Fri Jun 6 09:11:50 EDT 2003
Name: Kathy
Email:qluo@ust.hk URL:http:// Remote Host: ust.hk
Subject: paper
Dear Dr. Zuker,
Based on your web site you have a paper published in Nucleic Acids Res. 31(13) 1-10 (2003). However, I cannot find it from this journal. May you please let me know where this paper was published. Or if you have this paper in PDF format, may you please send it to me.
Thank you very much,
Kathy Luo
Hong Kong University of Science and Technology
Department of Biology
Hong Kong
M. Zuker replies:
The article will appear in July 2003.
Date: Tue Jun 10 10:18:58 EDT 2003
Name: bettina
Email:bettina.oberle@biotech.biol.ethz.ch URL:http:// Remote Host: biotech.biol.ethz.ch
Subject: RNA
Dear Professor Zuker,
I am very thankful for your homepage, helping desperate people like me finding reasons for the behavior of their sequences! thank you very much!
but, i've got (maybe small) problem:
I sent a batch job of my SARS spike protein last friday in order to recieve the eventual secondary structure of this sequence. unfortunately i didn't hear from you yet, there wasn't even an email notification in my mailbox, saying that the result will be sent some time. Did you get my batch job, or did I do something wrong?! If you got it, could you please tell me how long it still takes until I get the results?
thank you very much!
best regards,
bettina M. Zuker replies:
You submitted a single sequence of length 4920 on June 6 at 09-19-11 EDT. Your E-mail address was correctly entered. You should have received E-mail within a hour or so. You should save your job URL when you submit a batch job so that you can retrieve your results even if you do not receive an E-mail message. I have no idea of what went wrong. I have resubmitted your folding.
Date: Fri Jun 13 03:49:41 EDT 2003
Name: Pramod
Email:pyadava@hotmail.com URL:http:// Remote Host: rediffmail.com
Subject: targeted
I have been familiar with Michael Zucker's programs (FOLDRNA, dotplots, and MFOLD) since mid 80s (Iwas associated with Professor Martin Billeter in Zurich to cnstruct a recombinant RNA replicon based n phage Q$#223; RNA). Past 17 years have established the strength and monopoly of Michael in RNA folding. Hats off to Michael. Yet I do not know of a convenient program for modeling the 3-D structure of RNA. I wish Michael and his group all luck. M. Zuker replies:
Thank you. For atomic resolution 3-D modeling, try the Mc-Sym package by François Major.
Date: Fri Jun 13 04:38:40 EDT 2003
Name: Marc
Email:marc.colet@ulb.ac.be URL:http:// Remote Host: dbmarc.ulb.ac.be
Subject: mfold
I like the mfold package.
One question : could it be possible to configure the location of html ouput files when installing mfold package and also the URL to access those files. M. Zuker replies:
I do not understand your question. All output from mfold is deposited in the directory in which it is run. The input sequence should also be in this directory. When run in html mode (RUN_TYPE=html), three html files are created. The master file is 'name'.html, where 'name.seq' or 'name' is the name of the sequence file used for input. This file assumes that the other two html files and all the other output files are in the same directory. Image files are expected to be in $MFOLDLIB, which is an environment variable needed to run mfold. If $MFOLDLIB is not defined, then mfold expects to find them in $MFOLD/dat, where $MFOLD points to where the mfold package is installed. If you wish these files to be viewable over the world wide web, place them in a "public_html" (sub)directory, and define the environment variable "LIBDIR" (at the top of the mfold script) to point to where all the mfold energy data, images and other files are. $LIBDIR can be a directory or a URL.
Date: Tue Jun 24 04:03:52 EDT 2003
Name: Wen-Jun
Email:liact@yahoo.com URL:http:// Remote Host: 61.159.246.242
Subject: Please
>YIM70085
TTTATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGCTGAAGCTCCCAGCTTGCTGGGGGTGAATGAGTGGCGAACGGGTGAGTATCACGTGAGTAACCTGCCCTTAACTCTGGGATAAGCCCGGGAAACTGGGTCTAATACCGGATAGGACTGATCATCGCATGGTGGTTGGTTGAAAGTTTTTGACGGTTTTGGATGGACTCGCGGCCTATCAGTTTGTTGGTGGGGTAATGGCCTACCAAGGCTTTGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGGATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGTTGGGACGAAGCCCTTCGGGGTGACGGTACCTTCAGAAGAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTATCCGGAATTATTGGGCGTAAAGAGCTCGTAGGCGGTTTGTCACGTCTGCTGTGAAAGCTCGGGGCTTAACCTCGAGTTTGCAGTGGGTACGGGCAGGCTAGAGTGCAGTAGGGGAGACTGGAATTCCTGGTGTAGCGGTGAAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGGTCTCTGGGCTGTTACTGACGCTGAGGAGCGAAAGCATGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCATGCCGTAAACGTTGGGCACTAGGTGTGGGGAACATTTCCACGTTTTCCGCGCCGTAGCTAACGCATTAAGTGCCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGCGGATTAATTCGATGCAACGCGAAGAACCTTACCAAGGCTTGACATGCACTGGATCGCCCTAGAGATAGGGTTTCCCTTCGGGGCCGGTGTACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGGAACCCCTATTCTATGTTGCCAGCAATTCGGTTGGGGACTCATGGAAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGACGACGTCAAATCATCATGCCCCTTATGTCTTGGGCTTCACGCATGCTACAATGGCCGGCACAATGGGTTGCGAGACTGTGAGGTTGAGCTAATCCCATAAAACCGGTCTCAGTTCGGATTGGGGTCTGCAACTCGACCCCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCAAGTCACGAAAGTTGGTAACACCCGAAGCCGGTGGCCTAACCCTTTGTGGGGAGGAGCCGTCGAAGGTGGGACCGGTGATTGGGACTAAGTCGTAACAAGGTATCCGATCGAAAGGTCGG
M. Zuker replies: Please what?
Date: Tue Jun 24 20:55:07 EDT 2003
Name: Joe
Email:joe_chan@pacbell.net URL:http:// Remote Host: pacbell.net
Subject: delta
Dear Dr Zuker:
I enjoy learning secondary structure using your RNA folding server. I'm able to follow how to compute deltaG for hairpin, stacking and loops except the bulge loop with size equal to one.
I used the sequence "GUCCCUGGACCCAUGGAAUAGGACCC" and the Loop Free-Energy Decomposition page indicates that the free energy of bulge loop is 1.7. Would you please tell me how to obtain that number?
Sincerely, Joe Chan M. Zuker replies:
I assume that you mean the bulged C5 in the first folding:
10
-- C GA C
GUCC UG CC \
CAGG AU GG A
CC - AA U
20
The free energy increment for a bulge of size 1 is 3.8
kcal/mole according to the version 3.0
energy rules. However, for a bulge of 1, the stacking free energy of the base pairs on either side are also counted. In this case, it is the C5·G21/U6·A20 base pairs, with free energy -2.1 kcal/mole according to the stacking energies. The sum of these two energies is 1.7 kcal/mole. All of these rules are explained in detail in:
M. Zuker, D.H. Mathews & D.H. Turner.
Algorithms and Thermodynamics for RNA Secondary Structure Prediction:
A Practical Guide In RNA Biochemistry and Biotechnology,
11-43, J. Barciszewski and B.F.C. Clark, eds., NATO ASI Series, Kluwer
Academic Publishers, Dordrecht, NL, (1999)
See also: Loops
and Nearest neighbor rules (Note: 3 lines above equation (4)).
Date: Mon Jul 7 16:12:45 EDT 2003
Name: curt
Email:curt.balch@insightbb.com URL:http:// Remote Host: d-223-249.dhcp-129-79.indiana.edu
Subject: folding
no response to folding request- screen went blank M. Zuker replies:
According to the log files, you submitted a sequence of length 1290 to the mfold server today. Three submissions are recorded. All were rejected because you did not select "A batch" job for these long sequences. You can fold no more than 800 bases in an "immediate" folding.
Date: Wed Jul 16 16:27:17 EDT 2003
Name: Anonymous
Email:anonymous@someu.edu URL: Remote Host: someu.edu
Subject: RNA
Hi,
I recently began using the hybridization server and I find it very useful. I was wondering if you have a stand-alone installation for Linux available, as I intend to incorporate the functionality into a program which will get hybridization data many thousands of times. I have a copy of mfold 3.1.2 but I am unable to determine if the hybridization functionality is provided in this version.
Thank you for your attention to this matter.
Best regards M. Zuker replies:
My mfold 3.1.2 software contains all the programs needed to predict
2-state melting for hybridization. It lacks the script to tie things
together.
Using mfold software to compute such quantities is stupid and
inefficient. We have completely new software to compute hybridization and
melting that will be made available first on the web, and then by
license from RPI. This software computes full partition functions for
all two strand and single strand states. Everything is then put
together to compute ensemble free energies, heat capacities, UV
absorbance, and so on. Details of the method will appear in:
R.A. Dimitrov & M. Zuker.
Prediction of hybridization and melting for double stranded nucleic acids.
Biophysical J.85 (3) (in press), (2003)
As part of this package, simple programs to compute minimum free
energy were created. These simple programs, among other things,
compute two state melting for two strands of nucleic acid and for
single stranded nucleic acids. Take:
Note that the DNA energy files, licensed exclusively to DNA Software
of Ann Arbor, MI by Wayne State University, Detroit, are missing. You
must obtain these files either by obtaining an mfold license from
Washington University or by writing to John SantaLucia <jsl@chem.wayne.edu>. Copy
the .dgd and .dhd DNA energy files to the Dat subdirectory.
Date: Fri Jul 18 05:53:36 EDT 2003
Name: Ashish
Email:sashish@ibab.ac.in URL:http:// Remote Host: 203.197.163.194
Subject: Software
Sir,
I would like to know about the various types of software that predict the existence of hairpin complexes,quadruplexes present in DNA.Also I would like to know about the genetic algorithm followed by these programs.
Ashish Kumar Singh
Bangalore,India
Date: Tue Jul 22 10:14:46 EDT 2003
Name: Chris
Email:christopher.a.pettitt@gsk.com URL:http:// Remote Host: gsk.com
Subject: Lose
Hi Michael,
I have entered a search with 279 DNA oligo sequences into ZipFold however i only retrieve 268 in the results. Just thought you should know. M. Zuker replies: That's
odd. I count 280 sequences submitted today and I get 280 results when
I submit them myself. Please contact me if you experience this
problem again. Which sequences were missing?
Date: Wed Jul 23 05:34:29 EDT 2003
Name: Emin
Email:oezkan@embl.de URL: Remote Host: fw11v.embl-heidelberg.de
Subject: quickfold-zipfold
The zipfold and quickfold are great services but they lack a very very important feature that is the inability to give proper annotation to your sequences. I hope you will include this feature in the future. M. Zuker replies: What do you mean by "proper annotation"?
Date: Tue Aug 5 19:42:46 EDT 2003
Name: S
Email:spfletc@asu.edu URL:http:// Remote Host: samfletcher.dhcp.asu.edu
Subject: R
Date: Thu Aug 7 06:41:56 EDT 2003
Name: Jaakko
Email:Jaakko.Lumme@oulu.fi URL:http:// Remote Host: www-cache2.oulu.fi
Subject: Gyrodactylus
Thanks for the great service!
Date: Mon Aug 11 14:07:19 EDT 2003
Name: Email:iamacau@u.washington.edu URL:http:// Remote Host: d-128-95-123-154.dhcp4.washington.edu
Subject: problems
Trying to modify the image of a computed folding simply and repeatedly resulted in calling up the loop free-energy decomposition window despite several variou attempts to turn off or avoid this window. Any suggestions?
Date: Tue Aug 12 10:54:29 EDT 2003
Name: Timothy
Email:redbaron@jhmi.edu URL:http:// Remote Host: valued-b8cc434b.marburg1.jhmi.edu
Subject: changing
Hello Dr. Zuker,
I am a graduate student at Johns Hopkins in Baltimore, and I am designing experiments for which it would be useful to be able to change ionic strength and temperature parameters in mfold version 3.1. I have tried using version 2.3 as suggested on your site, but, presumably due to the use of new RNA parameters in v. 3.1, the two versions give me quite different structures for the same sequence.
Is there any way to alter temperature and ionic conditions in version 3.1? Is this feature on the way?
Thanks very much, not only for attending to this question, but for the wonderful program that you have provided.
Tim Hefferon
Human Genetics
Johns Hopkins Medicine
Date: Mon Aug 25 10:28:51 EDT 2003
Name: Tomas
Email:tomas.babak@utoronto.ca URL:http:// Remote Host: utoronto.ca
Subject: MFOLD
I really like the layout and ease of use of the server. However, lately it is only allowing me to fold about 1 to 2 sequences per day, before it gives the error message: "you have been banned from the server....please use quickfold" Quickfold runs into the same problems. Could you allow me to fold at least 50 sequences per day. I am not intending to run any batch jobs on it and respect the fact that there is danger of it being overused.
Thanks,
Tomas M. Zuker replies:
This is very strange. There are no restrictions to the use of the mfold
server. I did cut off someone who was folding hundreds of sequences of
length 1500 each day for weeks. You should be able to submit hundreds
of sequences a say, or many thousands to the quikfold server.
I'll try and track down the problem. You can help by reporting the exact time of such occurrences and by sending me the exact error message that you receive. Does the message appear on the web page, or is it sent to you in an E-mail message?
Date: Wed Aug 27 14:24:56 EDT 2003
Name: Sonja
Email:sonja.hundt@bio.uni-giessen.de URL:http:// Remote Host: max4-203.hrz.uni-giessen.de
Subject: RNA-folding
Dear Professor Zuker,
I like your web page but I am working with halophilic organisms and miss the possibility to fold RNA under salt concentrations other than 1 M NaCl. Is there any chance that this possibility will be there in the future?
With best wishes,
Sonja Hundt
Date: Sun Aug 31 16:24:34 EDT 2003
Name: Larry
Email:simpson@kdna.ucla.edu URL:http:// Remote Host: 164.67.60.204
Subject: Hi Mike,
How is it going?
Larry M. Zuker replies:
I'm surviving. How about you?
Date: Fri Sep 12 00:24:51 EDT 2003
Name: Bijaya
Email: URL:http:// Remote Host: dhcp-66-219.housing.utah.edu
Subject: great
I found this website pretty useful for folding RNA. But it is very difficult to find the links. If you please put all the links on your main page I guess lot of people will be benifited. For example, I could not find hybridization form. I urge you to put all the form under one main page so that it will be easy for us. M. Zuker replies:
All of the forms are accessable from the main page: http://www.bioinfo.rpi.edu/applications/mfold/,
as was recently reported in:
However, I agree with you that my personal and research pages are very much out-of-date and need new links so that people can easily find all of the different forms.
Date: Mon Sep 15 15:00:00 EDT 2003
Name: Antonio
Email:giraldez@saturn.med.nyu.edu URL:http:// Remote Host: mcnat125.med.nyu.edu
Subject: question
I have a question:
I'd like to send multiple sequences to predict their folding in a batch. Is there a way to include multiple seuquences in the same window in a fasta format and get the nice graphic output of the structure rather than the one form the fast folding. Thanks. M. Zuker replies:
Not yet. Sorry.
Date: Fri Sep 26 02:43:32 EDT 2003
Name: viswanadh
Email:viswanadh@biochem.iisc.ernet.in URL:http://biochem.iisc.ernet.in Remote Host: proxy.ece.iisc.ernet.in
Subject: a
sir, the main page was so much comfusing that we cant see what is there on the left side of the screen.
but its really nice that all programs for analysis of folding were kept in a place
good luck
viswanadh M. Zuker replies:
What "main page" are you referring to? I agree that my numerous web pages need to be reorganized.
Date: Wed Oct 8 17:21:53 EDT 2003
Name: Murugesan
Email:murugeg@ccf.org URL:http://www.clevelandclinic.org Remote Host: ccf.org
Subject: Use
Dear Prof. Zuker: I greatly appreciate this program that is freely available to the scientific community. Thanks to you and your colleagues. I am analyzing the same sequence (s) at increasing temperatures (2 degree increaments over 10 degrees) multiple times. Other parameters remain same (including email address). At present, I am copying and pasting each time in a new window and change the parameters again. I am wondering if it is possible to keep the same window and change only the required variable and reanalyze the same sequence again and again (without copying and pasting each time)to find the conditions free of secondary structures. Thank you for your attention. M. Zuker replies:
On the browser I most often use, I can use the "Back" button to return to the submission page and find the page as it was before clicking on the "Submit" ("Fold RNA" or "Fold DNA") button. I realize that this is not always true. I could open a new window for the results, but others might be unhappy. I'll have to think about it.
Why don't you download the form and fix the values of the parameters that won't be changing?
Date: Fri Oct 10 12:57:08 EDT 2003
Name: Murugesan
Email:murugeg@ccf.org URL:http://www.clevelandclinic.org Remote Host: ccf.org
Subject: Customized
Dear Prof. Zuker:
As you suggested, downloading the form and fixing the values has worked for us. Now, we have customized MFold window that allows us to do sequence analysis more efficiently. Thank you.
Date: Wed Oct 15 08:34:44 EDT 2003
Name: isabel
Email:isabel@mco.edu URL:http:// Remote Host: mco.edu
Subject: Comment
This is very useful Thanks!
Date: Thursday October 16 / Dydd Iau 16 Hydref 2003 06:56:49 EDT
Name: Jorge
Email:J.Garcia-Lara@sheffield.ac.uk URL:http:// Remote Host: dyn066088.shef.ac.uk
Subject: Thank
Thank you for providing such accessible and valuable resource.
Jorge Garcia-Lara
Department of Molecular Biology and Biotechnology
University of Sheffield
Date: Wed Oct 29 11:57:34 EST 2003
Name: G.
Email:murugeg@ccf.org URL:http://www.clevelandclinic.org Remote Host: ccf.org
Subject: Not
Dear Prof. Zuker: I am getting the following message when I try to do the secondary structure analysis of DNA.
"If you wish to hit the mfold server automatically, please
identify yourself. This mea ...." M. Zuker replies:
The large "scratch" disk on the bioinformatics web server filled up this morning. We know why. The problem should be solved by now (12:45 EST, October 29).
Date: Fri Nov 7 15:35:23 EST 2003
Name: Tom
Email:tomchou@ucla.edu URL:http:// Remote Host: ucla.edu
Subject: multiple
Hi. Nice server! Is there a way to input multiple pairs of
sequences to hybridize in the window at once? Or do I have to
test multiple hybridizations it by hand?
Cheers,
Tom
Date: Fri Dec 5 00:08:09 EST 2003
Name: robert
Email:robert@techfak.uni-bielefeld.de URL:http:// Remote Host: techfak.uni-bielefeld.de
Subject: DNA
Dear Michael,
greetings from Brisbane. I just tried the DNA hyridization server.
I get energies, and an empty box on the output page.
Is there going to be a representation of the optimal hybrid structure?
Regards
robert M. Zuker replies:
I just created a version that gives you an optimal hybridization. Use
this hyperlink. All of this will soon be replaced by better software.
Date: Thu Dec 18 03:16:31 EST 2003
Name: yang
Email:yangyc@bii-sg.org URL:http:// Remote Host: 202.90.17.4
Subject: Where
Dear Professor,
Thank you for creating such a wonderful tool for RNA 2ndary structure prediction. I am currently studying your online lecture on energy minimizing algorithm. I am wondering where can I find the energy tables indicated in the lecture. Thanks very much.
¤
Name: Gad
Email: gad.yagil@weizmann.ac.il
URL: http://www.weizmann.ac.il/~lcyagil
Remote Host: 212.199.184.47
Subject: contact
It was a pleasure meeting you 2 I hope you enjoyed the rest of your stay.
I wonder whether this continues to be the upto date site. If there
is now another one, please let me know. I shall soon try if I can find how to run with DNA Parameters, and let you know.
I am preparing a cover with the Yeast CEN4 paper I mentioned to you,
and other papers with the purine/pyrimidine tract story, i shall be glad to have your comments.
It was nice meeting you,
Gad
Name: L.MuthuSelvi
Email: selvimallax_82@hotmail.com
URL: http://
Remote Host: 210-210-32-47.lan.sify.net
Subject: structure
Respected Sir/Mam,
I wish to have the nice structure of the sequence
including all your calculations.What can I do?Kindly,provide me the possible suggestions!
Thank you.
Name: Maciej
Email:
URL:
Remote Host: pa157.opole.sdi.tpnet.pl
Subject: Solver
Your Pell Equation solver is great, thanks for making it.
Name: Mathew
Email: drmatz@rediffmail.com
URL: http://
Remote Host: ool-18bcbc3f.dyn.optonline.net
Subject: Hi
Sir,
I have gone through all your works.I am having a knowledge of both Computers as well as Biology especially Genetic.
I would happy to work animal related research you have.I am a veterinary doctor and a Major in Computer Science( expected by May 2002).
Please do the needful to guide me in my endeavour.
Thank you
Mathew Thomas
Name: Duleep
Email: dksam@iihr.kar.nic.in
URL: http://
Remote Host: iihr.kar.nic.in
Subject: Thanks
Respected Dr.Zuker, thanks for making this wonderful resource, I hope that by and by I will understand more and use better, with regards Samuel, Ind inst of Hort Research, Bangalore INDIA
Name: Tadeusz
Email: tmalin@insad.pl
URL: http://
Remote Host: isk.insad.pl
Subject: Many
Dear Professor Zuker,
I would like to say many, many thanks to you and to your co-workers
for creating and maintaining this wonderful service.
My first impression is that it is really great and I shall be happy to visit it again and again. It is wonderful that there are still some people sharing their achievements in a traditional way -
obviously having the satisfaction from providing help to the others.
It is good in a world nowadays.
With best wishes
Tadeusz Malinowski
Institute of Pomology and Floriculture, Skierniewice, Poland
Name: Eitan
Email: bcbibi@wicc.weizmann.ac.il
URL: http://
Remote Host: 212.199.50.186
Subject: Great
Name: Rupali
Email: ruparbhane@yahoo.com
URL: http://
Remote Host: rupali
Subject: Wonderful
Dear Prof. Zuker,
Many thanks for developing such a wonderful site. This site is very useful for people working in the RNA folding.
From Beginners to Advance Learners, each one will be beneficial.
Sincerely,
Rupali.
Name: Leonid
Email: leonid_buryanovskyy@nymc.edu
URL: http://
Remote Host: ns2.nymc.edu
Subject:
Great site. Thanks for the very good service. Although I am quite a beginner, the program is very convenient.
Leo
Name: Sergeant
Email: alain.sergeant@ens-lyon.fr
URL: http://
Remote Host: 140.77.192.33
Subject: publication
Dear Dr Zuker,
Am I allowed to include in a publication pictures of RNA folding obtained through your web si!te, and what shall I cite if allowed.
Thanks for your answer
Very sincerely,
Alain Sergeant
PhD, DR1 CNRS
M. Zuker replies: Yes, you are allowed to use any of the images that are created for any of your foldings. I have submitted an article that is targeted for a special issue of Nucleic Acids Research that will deal with web servers. In the mean time, please cite the articles that are cited on this page.
Name: Morgane
Email: morgane@get2net.dk
URL: http://
Remote Host: p422-016.ppp.get2net.dk
Subject:
This is one of the most helpfull sites I have come across. Thank you so much to Dr Zuker and his co-workers for creating and maintaining this resource! If I may, allow me to correct an insignificant detail: the link to the French version of this page should read "Cette page...", not "Ce page...".
Morgane Thomsen, Copenhagen.
M. Zuker replies: Thanks for the tip. The French version is now corrected.
Name: xiaoying
Email: xiaoying.chen@roche.com
URL: http://
Remote Host: p196-3-48-10.pal.roche.com
Subject: batch
Dear Dr. Zucker,
Can we submit multiple sequences in a single batch submission? or in any way?
Thanks,
--xiaoying
M. Zuker replies: You may submit many (hundreds) of sequences in a single submission using the quikfold or zipfold servers. The quikfold server gives no graphics. The zipfold server gives only minimum free energies. Sequence size is limited and only "immediate jobs" are allowed.
URLS: quikfold server zipfold server
Name: guanyuan
Email: guanyuan008@hotmail.com
URL: http://
Remote Host: hotmail.com
Subject: It's
I'm a real freshman in this domain, and I found this is a real wonderful web for studying RNA. But I still don't Kown the meaning of some of the information in Thermal details.
Name: Arnold
Email: sciarnold@yahoo.com
URL: http://
Remote Host: upchdat.upch.edu.pe
Subject: Complaint
Dear Professor Michael Zuker,
I have used your server to calculate the Tm of the secundary structure of my predicted PCR product about a week a go. Today, March 21st, I made a check of these values and I found that most of them have changed. Some of them in about 6 degrees, that is really important for the experiment I shall carry. Why does that happens?.
Another issue is that I don't understand the reason to ask for a folding temperature when one just wants to know the Tm of a oligonucleotide sequence.
Yours faithfully.
-Arnold Pérez Goicochea
Name: Markus
Email: Markus.Boehl@chemie.tu-dresden.de
URL: http://
Remote Host: cbcp49.chm.tu-dresden.de
Subject: What's
Dear Mr. Zuker....
....mfold is really a great tool for our needs, we use it intensively, but I was looking for one information I was not able to find on the hole mfold page. What is the dimension of your energy calculation?? Is it kJ/mol or Kcal/mol???
Thanks for the possibilty to use mfold....and best wishes from Dresden
Markus Boehl
M. Zuker replies: The units are, and have always been, kcal/mol (not Kcal).
Name: kavitha
Email: kavithareddyk@yahoo.com
URL: http://
Remote Host: 61.1.164.144
Subject: suggestion
i guess some detailed lecture notes on each related program would help more in understanding
Name:
Email:
URL: http://
Remote Host: imsb47-247.mbio.au.dk
Subject:
Concerning the Hybridization Server:
It would be useful if the total nucleic acid concentration could be given in uM or pM, since it can be entered in the form. The 'problem' is that the program accepts that you write uM/pM, but then still calculates as if the concentration were given in mM or M.
-Otherwise thank you for a very usefull website!
Name: Nicholas
Email: nmills@itsa.ucsf.edu
URL:
Remote Host: udp021988uds.ucsf.edu
Subject: Maximum
We are currently pursuing an idea in which we would like to fold a large number of DNA sequences in the promoter regions of different genes. Do you have any suggestions for submitting large numbers of DNA sequences? As a first pass, energy values alone would be valuable.
Thanks
Nicholas Mills
UCSF Dept. of Biochemistry
M. Zuker replies: You may fold hundreds of DNA or RNA sequences at a time using related servers.
Name: Esther
Email:
URL: http://
Remote Host: mednet.ucla.edu
Subject: Thanks!
Hi,
Found your website to be very useful and fairly user friendly.
I learned of it through BioRAD. Would have liked to learn more
about the other variables (like what they mean).
Thanks again.
Name: LiuFei
Email: liufei@itp.ac.cn
URL: http://
Remote Host: 159.226.161.109
Subject: hybridization
Dear Dr. Zuker,
Is the hybridization algorithm in your web also based on a minimum free energy (mfe)? Or are two strands viewed as two parts of one single-strand DNA (RNA) and just some constraints added?
M. Zuker replies: The existing hybridization algorithm is based on minimum free energy at some (arbitrary temperature). The default temperature is 55 °C. The melting temperature, Tm, is based on a simple two-state model that assumes either complete hybridization at minimum free energy or total separation of the two strands. No intermediates are considered. Hybridization is computed for two separate strands of DNA or RNA. In initiation free energy is used to bring the two strands together.
Name: Peter
Email: Peter.Weekers@rug.ac.be
URL: http://
Remote Host: molphylo.rug.ac.be
Subject: MFOLD
Hi Mike,
Once again I had to use your magnificent MFOLD program. As before, it works wonderful. Thanks again for this very nice facility.
Cheers,
Peter
Name: Jiong
Email: jiong.zhang@stjude.org
URL: http://
Remote Host: gatekeeper.stjude.org
Subject: query
Hi, thanks for the wonderful web server. I have a large number of oligos (40-60 bases long) that I would like to look for hairpin loops. But I don't want to swamp your server. What is the limit on the number of short sequences that I can submit? Thanks.
M. Zuker replies: There is no limit. Do your worst. I dare you. (However, if you really mess up the server, you will be blocked from the site until you moderate your requests.) If you are just looking for haipins in a (large) number of oligos, then you should be using my "quikfold" server. You can submit up to about 1000 sequences in a single run.
Name: Stella
Email: casinos@casinos-casino.org
URL:
Remote Host: afontenayssb-109-1-1-173.abo.wanadoo.fr
Subject: great
Hello, i live in France, and i studied a little bit all about DNA, and also chemicals formulas. I admire your job as i know how difficult it is to analyse such human elementaries bricks. Thanks to your work, may be genetic therapy, in a futur, will be a great solution. so thanks for your studies of Acid Ribonucleic,..
Name: mark
Email:
URL: http://
Remote Host: bh23218.umsl.edu
Subject: at
I'm at a Univ.MO-St. Louis computer, can't complete assignment to visualize RNA folding sequence. Can't download mfold, can't display any image. Wasting too much time.
Name: shiri
Email: shirimazor@hotmail.com
URL: http://
Remote Host: diup-13-175.inter.net.il
Subject: using
Mr. Zuker,
im only a young biology student, but manage your program and i want to thank u for creating such a usfull, easy and reliable program.
Name: Allison
Email: allison@bio-alliance.com
URL: http://www.bio-alliance.com
Remote Host: rrcs-west-24-24-135-247.biz.rr.com
Subject: Your
Love your Bar-Mitzvah picture.
Allison
M. Zuker replies: Thanks, except you're off by 11 years. I'm 24 years old in that picture and attending a friend's wedding.
Name: David
Email: dmcohen@mail.uh.edu
URL: http://
Remote Host: 129-7-197-241.dhcp.uh.edu
Subject: my
I enter the following 5 sequences in the window of the TM server:
AGGTGAACTGCAAATACATAGGGACTGATGCCTTCCACTTCCTCTGC;
TGAAGCTGAAAGACCATCTTCAGTGACACCTCCTGCAATCACAATTT;
ACACTAGCGCAGTTATCCTACACAAGGCATCTCCGATTCTCCAGTCA;
AGAGAGAAAGGGAGGGCAAGGGAGAAGGGAGAAGGGAAGAGAGAAAC;
ACTTTAAGCATTGGATCATAGGTTGTGGGTGCCATAGGAGAGGTGGG;
However, I only get information (dG, dS, dH, and Tm) on 4 of them!
Can you tell me why ? This is important to people with thousands of short sequences, such as myself.
Thanks.
David Cohen
Here is the output:
may23_#9 is the 3588719th group of nucleic acid sequences folded on the Rouillard server.
- vendredi 23 mai 2003 18:00:37 EDT / divendres 23 mai 2003 18:00:37 EDT -
Folding may23_#9 at 37° C. ()
[Na+] = 1.0 M, [Mg++] = 0.0 M, oligo correction
- Computed for 129-7-197-241.dhcp.uh.edu -
- Output -
Computed free energies
1. dG = -0.9 dH = -16.1 dS = -49.0 Tm = 55.4
2. dG = -2.9 dH = -79.3 dS = -246.3 Tm = 48.8
3. dG = -1.7 dH = -39.3 dS = -121.2 Tm = 51.0
4. dG = -0.6 dH = -29.0 dS = -91.6 Tm = 43.6
These computations were performed on cn-20.bioinfo.z in 0 min. and 0.26 sec. The results have already been erased.
M. Zuker replies: Your third sequence has no possible folding, so results are not given for it. There is no possible secondary structure because there is no possibility to have at least one pair of consecutive base pairs. I solved this problem a while ago with the version of the server that most people hit directly using a script. I've switched over to this plain output. You'll see that missing sequences are clearly indicated because the sequence numbering will jump by more than one. Try it out and give me your opinion.
Name: Anna
Email: mastrangelo@iscfoggia.it
URL: http://
Remote Host: host202-120.pool80105.interbusiness.it
Subject: folding
I'm working on plant UTR. Is it possible to change the temperature value which is fixed at 37°C?
M. Zuker replies: Yes, it is possible, but you must use the older RNA energy parameters. Go to RNA mfold version 2.3 server.
Name: Kathy
Email: qluo@ust.hk
URL: http://
Remote Host: ust.hk
Subject: paper
Dear Dr. Zuker,
Based on your web site you have a paper published in Nucleic Acids Res. 31(13) 1-10 (2003). However, I cannot find it from this journal. May you please let me know where this paper was published. Or if you have this paper in PDF format, may you please send it to me.
Thank you very much,
Kathy Luo
Hong Kong University of Science and Technology
Department of Biology
Hong Kong
M. Zuker replies: The article will appear in July 2003.
Name: bettina
Email: bettina.oberle@biotech.biol.ethz.ch
URL: http://
Remote Host: biotech.biol.ethz.ch
Subject: RNA
Dear Professor Zuker,
I am very thankful for your homepage, helping desperate people like me finding reasons for the behavior of their sequences! thank you very much!
but, i've got (maybe small) problem:
I sent a batch job of my SARS spike protein last friday in order to recieve the eventual secondary structure of this sequence. unfortunately i didn't hear from you yet, there wasn't even an email notification in my mailbox, saying that the result will be sent some time. Did you get my batch job, or did I do something wrong?! If you got it, could you please tell me how long it still takes until I get the results?
thank you very much!
best regards,
bettina
M. Zuker replies: You submitted a single sequence of length 4920 on June 6 at 09-19-11 EDT. Your E-mail address was correctly entered. You should have received E-mail within a hour or so. You should save your job URL when you submit a batch job so that you can retrieve your results even if you do not receive an E-mail message. I have no idea of what went wrong. I have resubmitted your folding.
Name: Pramod
Email: pyadava@hotmail.com
URL: http://
Remote Host: rediffmail.com
Subject: targeted
I have been familiar with Michael Zucker's programs (FOLDRNA, dotplots, and MFOLD) since mid 80s (Iwas associated with Professor Martin Billeter in Zurich to cnstruct a recombinant RNA replicon based n phage Q$#223; RNA). Past 17 years have established the strength and monopoly of Michael in RNA folding. Hats off to Michael. Yet I do not know of a convenient program for modeling the 3-D structure of RNA. I wish Michael and his group all luck.
M. Zuker replies: Thank you. For atomic resolution 3-D modeling, try the Mc-Sym package by François Major.
Name: Marc
Email: marc.colet@ulb.ac.be
URL: http://
Remote Host: dbmarc.ulb.ac.be
Subject: mfold
I like the mfold package.
One question : could it be possible to configure the location of html ouput files when installing mfold package and also the URL to access those files.
M. Zuker replies: I do not understand your question. All output from mfold is deposited in the directory in which it is run. The input sequence should also be in this directory. When run in html mode (RUN_TYPE=html), three html files are created. The master file is 'name'.html, where 'name.seq' or 'name' is the name of the sequence file used for input. This file assumes that the other two html files and all the other output files are in the same directory. Image files are expected to be in $MFOLDLIB, which is an environment variable needed to run mfold. If $MFOLDLIB is not defined, then mfold expects to find them in $MFOLD/dat, where $MFOLD points to where the mfold package is installed. If you wish these files to be viewable over the world wide web, place them in a "public_html" (sub)directory, and define the environment variable "LIBDIR" (at the top of the mfold script) to point to where all the mfold energy data, images and other files are. $LIBDIR can be a directory or a URL.
Name: Wen-Jun
Email: liact@yahoo.com
URL: http://
Remote Host: 61.159.246.242
Subject: Please
>YIM70085
TTTATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGCTGAAGCTCCCAGCTTGCTGGGGGTGAATGAGTGGCGAACGGGTGAGTATCACGTGAGTAACCTGCCCTTAACTCTGGGATAAGCCCGGGAAACTGGGTCTAATACCGGATAGGACTGATCATCGCATGGTGGTTGGTTGAAAGTTTTTGACGGTTTTGGATGGACTCGCGGCCTATCAGTTTGTTGGTGGGGTAATGGCCTACCAAGGCTTTGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGGATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGTTGGGACGAAGCCCTTCGGGGTGACGGTACCTTCAGAAGAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTATCCGGAATTATTGGGCGTAAAGAGCTCGTAGGCGGTTTGTCACGTCTGCTGTGAAAGCTCGGGGCTTAACCTCGAGTTTGCAGTGGGTACGGGCAGGCTAGAGTGCAGTAGGGGAGACTGGAATTCCTGGTGTAGCGGTGAAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGGTCTCTGGGCTGTTACTGACGCTGAGGAGCGAAAGCATGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCATGCCGTAAACGTTGGGCACTAGGTGTGGGGAACATTTCCACGTTTTCCGCGCCGTAGCTAACGCATTAAGTGCCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGCGGATTAATTCGATGCAACGCGAAGAACCTTACCAAGGCTTGACATGCACTGGATCGCCCTAGAGATAGGGTTTCCCTTCGGGGCCGGTGTACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGGAACCCCTATTCTATGTTGCCAGCAATTCGGTTGGGGACTCATGGAAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGACGACGTCAAATCATCATGCCCCTTATGTCTTGGGCTTCACGCATGCTACAATGGCCGGCACAATGGGTTGCGAGACTGTGAGGTTGAGCTAATCCCATAAAACCGGTCTCAGTTCGGATTGGGGTCTGCAACTCGACCCCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCAAGTCACGAAAGTTGGTAACACCCGAAGCCGGTGGCCTAACCCTTTGTGGGGAGGAGCCGTCGAAGGTGGGACCGGTGATTGGGACTAAGTCGTAACAAGGTATCCGATCGAAAGGTCGG M. Zuker replies: Please what?
Name: Joe
Email: joe_chan@pacbell.net
URL: http://
Remote Host: pacbell.net
Subject: delta
Dear Dr Zuker:
I enjoy learning secondary structure using your RNA folding server. I'm able to follow how to compute deltaG for hairpin, stacking and loops except the bulge loop with size equal to one.
I used the sequence "GUCCCUGGACCCAUGGAAUAGGACCC" and the Loop Free-Energy Decomposition page indicates that the free energy of bulge loop is 1.7. Would you please tell me how to obtain that number?
Sincerely, Joe Chan
M. Zuker replies: I assume that you mean the bulged C5 in the first folding:
10 -- C GA C GUCC UG CC \ CAGG AU GG A CC - AA U 20The free energy increment for a bulge of size 1 is 3.8 kcal/mole according to the version 3.0 energy rules. However, for a bulge of 1, the stacking free energy of the base pairs on either side are also counted. In this case, it is the C5·G21/U6·A20 base pairs, with free energy -2.1 kcal/mole according to the stacking energies. The sum of these two energies is 1.7 kcal/mole. All of these rules are explained in detail in:M. Zuker, D.H. Mathews & D.H. Turner.
Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide In RNA Biochemistry and Biotechnology, 11-43, J. Barciszewski and B.F.C. Clark, eds., NATO ASI Series, Kluwer Academic Publishers, Dordrecht, NL, (1999)
See also: Loops and Nearest neighbor rules (Note: 3 lines above equation (4)).
Name: curt
Email: curt.balch@insightbb.com
URL: http://
Remote Host: d-223-249.dhcp-129-79.indiana.edu
Subject: folding
no response to folding request- screen went blank
M. Zuker replies: According to the log files, you submitted a sequence of length 1290 to the mfold server today. Three submissions are recorded. All were rejected because you did not select "A batch" job for these long sequences. You can fold no more than 800 bases in an "immediate" folding.
Name: Anonymous
Email: anonymous@someu.edu
URL:
Remote Host: someu.edu
Subject: RNA
Hi,
I recently began using the hybridization server and I find it very useful. I was wondering if you have a stand-alone installation for Linux available, as I intend to incorporate the functionality into a program which will get hybridization data many thousands of times. I have a copy of mfold 3.1.2 but I am unable to determine if the hybridization functionality is provided in this version.
Thank you for your attention to this matter.
Best regards
M. Zuker replies: My mfold 3.1.2 software contains all the programs needed to predict 2-state melting for hybridization. It lacks the script to tie things together.
Using mfold software to compute such quantities is stupid and inefficient. We have completely new software to compute hybridization and melting that will be made available first on the web, and then by license from RPI. This software computes full partition functions for all two strand and single strand states. Everything is then put together to compute ensemble free energies, heat capacities, UV absorbance, and so on. Details of the method will appear in:
R.A. Dimitrov & M. Zuker.
Prediction of hybridization and melting for double stranded nucleic acids.
Biophysical J. 85 (3) (in press), (2003)
As part of this package, simple programs to compute minimum free energy were created. These simple programs, among other things, compute two state melting for two strands of nucleic acid and for single stranded nucleic acids. Take:
http://www.rpi.edu/~zukerm/export/OligoArrayAux-1.4.tar.gz
Note that the DNA energy files, licensed exclusively to DNA Software of Ann Arbor, MI by Wayne State University, Detroit, are missing. You must obtain these files either by obtaining an mfold license from Washington University or by writing to John SantaLucia <jsl@chem.wayne.edu>. Copy the .dgd and .dhd DNA energy files to the Dat subdirectory.
Name: Ashish
Email: sashish@ibab.ac.in
URL: http://
Remote Host: 203.197.163.194
Subject: Software
Sir,
I would like to know about the various types of software that predict the existence of hairpin complexes,quadruplexes present in DNA.Also I would like to know about the genetic algorithm followed by these programs.
Ashish Kumar Singh
Bangalore,India
Name: Chris
Email: christopher.a.pettitt@gsk.com
URL: http://
Remote Host: gsk.com
Subject: Lose
Hi Michael,
I have entered a search with 279 DNA oligo sequences into ZipFold however i only retrieve 268 in the results. Just thought you should know.
M. Zuker replies: That's odd. I count 280 sequences submitted today and I get 280 results when I submit them myself. Please contact me if you experience this problem again. Which sequences were missing?
Name: Emin
Email: oezkan@embl.de
URL:
Remote Host: fw11v.embl-heidelberg.de
Subject: quickfold-zipfold
The zipfold and quickfold are great services but they lack a very very important feature that is the inability to give proper annotation to your sequences. I hope you will include this feature in the future.
M. Zuker replies: What do you mean by "proper annotation"?
Name: S
Email: spfletc@asu.edu
URL: http://
Remote Host: samfletcher.dhcp.asu.edu
Subject: R
Name: Jaakko
Email: Jaakko.Lumme@oulu.fi
URL: http://
Remote Host: www-cache2.oulu.fi
Subject: Gyrodactylus
Thanks for the great service!
Name:
Email: iamacau@u.washington.edu
URL: http://
Remote Host: d-128-95-123-154.dhcp4.washington.edu
Subject: problems
Trying to modify the image of a computed folding simply and repeatedly resulted in calling up the loop free-energy decomposition window despite several variou attempts to turn off or avoid this window. Any suggestions?
Name: Timothy
Email: redbaron@jhmi.edu
URL: http://
Remote Host: valued-b8cc434b.marburg1.jhmi.edu
Subject: changing
Hello Dr. Zuker,
I am a graduate student at Johns Hopkins in Baltimore, and I am designing experiments for which it would be useful to be able to change ionic strength and temperature parameters in mfold version 3.1. I have tried using version 2.3 as suggested on your site, but, presumably due to the use of new RNA parameters in v. 3.1, the two versions give me quite different structures for the same sequence.
Is there any way to alter temperature and ionic conditions in version 3.1? Is this feature on the way?
Thanks very much, not only for attending to this question, but for the wonderful program that you have provided.
Tim Hefferon
Human Genetics
Johns Hopkins Medicine
Name: Tomas
Email: tomas.babak@utoronto.ca
URL: http://
Remote Host: utoronto.ca
Subject: MFOLD
I really like the layout and ease of use of the server. However, lately it is only allowing me to fold about 1 to 2 sequences per day, before it gives the error message: "you have been banned from the server....please use quickfold" Quickfold runs into the same problems. Could you allow me to fold at least 50 sequences per day. I am not intending to run any batch jobs on it and respect the fact that there is danger of it being overused.
Thanks,
Tomas
M. Zuker replies: This is very strange. There are no restrictions to the use of the mfold server. I did cut off someone who was folding hundreds of sequences of length 1500 each day for weeks. You should be able to submit hundreds of sequences a say, or many thousands to the quikfold server.
I'll try and track down the problem. You can help by reporting the exact time of such occurrences and by sending me the exact error message that you receive. Does the message appear on the web page, or is it sent to you in an E-mail message?
Name: Sonja
Email: sonja.hundt@bio.uni-giessen.de
URL: http://
Remote Host: max4-203.hrz.uni-giessen.de
Subject: RNA-folding
Dear Professor Zuker,
I like your web page but I am working with halophilic organisms and miss the possibility to fold RNA under salt concentrations other than 1 M NaCl. Is there any chance that this possibility will be there in the future?
With best wishes,
Sonja Hundt
Name: Larry
Email: simpson@kdna.ucla.edu
URL: http://
Remote Host: 164.67.60.204
Subject:
Hi Mike,
How is it going?
Larry
M. Zuker replies: I'm surviving. How about you?
Name: Bijaya
Email:
URL: http://
Remote Host: dhcp-66-219.housing.utah.edu
Subject: great
I found this website pretty useful for folding RNA. But it is very difficult to find the links. If you please put all the links on your main page I guess lot of people will be benifited. For example, I could not find hybridization form. I urge you to put all the form under one main page so that it will be easy for us.
M. Zuker replies: All of the forms are accessable from the main page:
http://www.bioinfo.rpi.edu/applications/mfold/, as was recently reported in:
M. Zuker
Mfold web server for nucleic acid folding and hybridization prediction.
Nucleic Acids Res. 31 (13), 3406-15, (2003)
[Abstract] [Full Text] [Supplementary Material] [Additional Information]
However, I agree with you that my personal and research pages are very much out-of-date and need new links so that people can easily find all of the different forms.
Name: Antonio
Email: giraldez@saturn.med.nyu.edu
URL: http://
Remote Host: mcnat125.med.nyu.edu
Subject: question
I have a question:
I'd like to send multiple sequences to predict their folding in a batch. Is there a way to include multiple seuquences in the same window in a fasta format and get the nice graphic output of the structure rather than the one form the fast folding. Thanks.
M. Zuker replies: Not yet. Sorry.
Name: viswanadh
Email: viswanadh@biochem.iisc.ernet.in
URL: http://biochem.iisc.ernet.in
Remote Host: proxy.ece.iisc.ernet.in
Subject: a
sir, the main page was so much comfusing that we cant see what is there on the left side of the screen.
but its really nice that all programs for analysis of folding were kept in a place
good luck
viswanadh
M. Zuker replies: What "main page" are you referring to? I agree that my numerous web pages need to be reorganized.
Name: Murugesan
Email: murugeg@ccf.org
URL: http://www.clevelandclinic.org
Remote Host: ccf.org
Subject: Use
Dear Prof. Zuker: I greatly appreciate this program that is freely available to the scientific community. Thanks to you and your colleagues. I am analyzing the same sequence (s) at increasing temperatures (2 degree increaments over 10 degrees) multiple times. Other parameters remain same (including email address). At present, I am copying and pasting each time in a new window and change the parameters again. I am wondering if it is possible to keep the same window and change only the required variable and reanalyze the same sequence again and again (without copying and pasting each time)to find the conditions free of secondary structures. Thank you for your attention.
M. Zuker replies: On the browser I most often use, I can use the "Back" button to return to the submission page and find the page as it was before clicking on the "Submit" ("Fold RNA" or "Fold DNA") button. I realize that this is not always true. I could open a new window for the results, but others might be unhappy. I'll have to think about it.
Why don't you download the form and fix the values of the parameters that won't be changing?
Name: Murugesan
Email: murugeg@ccf.org
URL: http://www.clevelandclinic.org
Remote Host: ccf.org
Subject: Customized
Dear Prof. Zuker:
As you suggested, downloading the form and fixing the values has worked for us. Now, we have customized MFold window that allows us to do sequence analysis more efficiently. Thank you.
Name: isabel
Email: isabel@mco.edu
URL: http://
Remote Host: mco.edu
Subject: Comment
This is very useful Thanks!
Name: Jorge
Email: J.Garcia-Lara@sheffield.ac.uk
URL: http://
Remote Host: dyn066088.shef.ac.uk
Subject: Thank
Thank you for providing such accessible and valuable resource.
Jorge Garcia-Lara
Department of Molecular Biology and Biotechnology
University of Sheffield
Name: G.
Email: murugeg@ccf.org
URL: http://www.clevelandclinic.org
Remote Host: ccf.org
Subject: Not
Dear Prof. Zuker: I am getting the following message when I try to do the secondary structure analysis of DNA.
"If you wish to hit the mfold server automatically, please
identify yourself. This mea ...."
M. Zuker replies: The large "scratch" disk on the bioinformatics web server filled up this morning. We know why. The problem should be solved by now (12:45 EST, October 29).
Name: Tom
Email: tomchou@ucla.edu
URL: http://
Remote Host: ucla.edu
Subject: multiple
Hi. Nice server! Is there a way to input multiple pairs of
sequences to hybridize in the window at once? Or do I have to
test multiple hybridizations it by hand?
Cheers,
Tom
Name: robert
Email: robert@techfak.uni-bielefeld.de
URL: http://
Remote Host: techfak.uni-bielefeld.de
Subject: DNA
Dear Michael,
greetings from Brisbane. I just tried the DNA hyridization server.
I get energies, and an empty box on the output page.
Is there going to be a representation of the optimal hybrid structure?
Regards
robert
M. Zuker replies: I just created a version that gives you an optimal hybridization. Use this hyperlink. All of this will soon be replaced by better software.
Name: yang
Email: yangyc@bii-sg.org
URL: http://
Remote Host: 202.90.17.4
Subject: Where
Dear Professor,
Thank you for creating such a wonderful tool for RNA 2ndary structure prediction. I am currently studying your online lecture on energy minimizing algorithm. I am wondering where can I find the energy tables indicated in the lecture. Thanks very much.
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