Date: Fri Jan 9 16:23:05 EST 2009
Name: Ryan Morin Email: rmorin@bcgsc.ca URL: http:// Remote Host: pat.bcgsc.ca Subject: Bug with latest version of mfold server? Hi. I am trying to add some highlighted bases in a piece of RNA sequence I am folding. Everything is set to default except for the 'highlight' box, which I put a few numbers separated by a comma. This used to work (highlight the individual bases in the list) but now I am getting strange behaviour (it is treated as a range of some sort). Is there a new feature I am failing to understand, or has the usage somehow changed? Thanks Regards, Ryan M. Zuker replies: You are using incorrect syntax to describe regions to be annotated. For a single continuous region, say 10 to 23 inclusive, use "10-23" (without quotes). For a single nucleotide, you must enter, for example, "10-10". If you wish to annotate more than one region, separate the regions using a comma. For example, "10-10, 23-31, 54-60". 
Date: Tue Jan 20 17:53:26 EST 2009
Name: Puranjoy Bhattacharjee Email: puran@cs.vt.edu URL: http:// Remote Host: tolstoy.cs.vt.edu Subject: Output files from hybrid2.pl Dear Dr. Zuker, Is there a manual/web-page describing the contents of various files output by hybrid2.pl? In particular, I am interested in the distinction between the free energies in files of type "target-probe.dG" and "target-probe.AB.dG", if I had used "target.seq" and "probe.seq" as inputs. I read that the second contains "free energy of formation of a species". Is that correct, and what is the significance? Thanks a lot, Puranjoy
Date: Wed Jan 21 16:42:38 EST 2009
Name: Nanting Ni Email: nni3@student.gsu.edu URL: http:// Remote Host: ga-2p4jr8d24n7i.gsu.edu Subject: It works very well. Thanks a lot!!
Date: Mon Feb 9 15:45:39 EST 2009
Name: Sunita Koul Email: sunita@pathology.wustl.edu URL: http:// Remote Host: IP-11-183.wustl.edu Subject: Coverting to bracket notation I currently using the UNAFOlD program for folding. Now the end user wants to see the results in Vienna bracket notation. Is their a utility that will do it for me. M. Zuker replies: Download the Perl script, Ct2B.pl. It accepts standard input or else use as 'Ct2B.pl file.ct'. Output is standard out. It's very simple.
Date: Wed Feb 11 12:45:28 EST 2009
Name: Sunita Koul Email: URL: http:// Remote Host: IP-11-183.wustl.edu Subject: Thanks Thanks a lot for the utility. It works great 
Date: Fri Feb 13 15:18:07 EST 2009
Name: anna korakova Email: anna.korakova1@gmail.com URL: Remote Host: ool-457f017d.dyn.optonline.net Subject: Former student of yours, just thought I'd say Hi Hello, I used to be your student and just visited the site to see who I can find here. I must say I really enjoyed learning from you and thank you for your help in everything!
Date: Sun Mar 15 18:52:52 EDT 2009
Name: micky mouse Email: m.mouse@cheese.net URL: http:// Remote Host: vpn-210-8.net.rpi.edu Subject: hi hi 
Date: Wed Mar 18 10:58:02 EDT 2009
Name: Alfonso Soler Email: URL: http:// Remote Host: 98-235-126-200.fibertel.com.ar Subject: Great program The program has been of great help to me. Thanks a lot! I'd like to know if there is a way to increase the numbers of nucleotides in the folded diagram thanks! 
Date: Sun Apr 12 04:23:41 EDT 2009
Name: Yi Zhang Email: zhaqi1972@163.com URL: http:// Remote Host: 172.188.223.222.broad.sj.he.dynamic.163data.com.cn Subject: Doctor we are studying locust's miRNA, hope to get the target mRNA in your website, thank you for your contribution in this field! If we have any questions, we shall contact with you. 
Date: Wed Apr 15 12:32:52 EDT 2009
Name: Angie Biba Email: angeliki.biba@ccc.ox.ac.uk URL: http:// Remote Host: abiba.imm.ox.ac.uk Subject: Which averaging window Dear Dr Zuker, I am using mfold to fold the mRNA of the the ε-subunit of the ACh receptor. It is working nicely. It is ~2.5 kb and I leave it at default for the window option, which, if I've got it right, must mean that the window is set to 25. When I get the results however, I don't know which averaging window I should use for the view ss-count feature. I am trying to see the probabilities of a base to be single or paired in the 31 folding that were predicted and the differences between window 1 and 25 are very big and I don't know what I should report. Am I doing something wrong? I guess I have not understand the function of "window", though I read the definition. If you can help me it would be hugely appreciated. Thank you very much! Angie 
Date: Wed Apr 15 22:39:03 EDT 2009
Name: Na Email: liunasophia@yahoo.com.cn URL: http:// Remote Host: zx.mskcc.org Subject: UNAFold has a deficiency Dear professor, I downloaded UNAFold software and run it in my computer. I found there are only 3 choices for --ann . Why "high light" is not concluded in command option "--ann=(none | p-num | ss-count) (defaults to none) ". I hope certain continuous bases in the structure displayed in the output .ps file can be colored. (This can be successfully achieved by using mfold server, how can I achieve this in my own computer while running your UNAFold?) Sincerely look forward to your reply. Regards Na
Date: Fri Apr 24 13:49:41 EDT 2009
Name: Nicholas Price Email: price4890@gmail.com URL: http:// Remote Host: 75-148-137-210-Houston.hfc.comcastbusiness.net Subject: RNAfold question Hi Michael I am using the RNAfold function (Vienna package) to look at RNA structures in C.elegans. For some of the Rna sequences however I only get a loop structure ex:UACAAAGUAUUUGAAAAGUCGUGC. Is that a false prediction of the function??? Thanks allot Nicholas M. Zuker replies:I don't know what you mean by a "loop structure", but I can easily guess. You mean "no structure". If I run your sequence through Vienna package RNAfold program, I get an empty folding. If I run it through our UNAFold package (hybrid-ss-min run in "mfold" mode), I get four different foldings; all of them unstable (at 37 deg C):
dG = 0.8
10
UACAAA -- G
GUAU UU A
CGUG GA A
------ CU A
20
dG = 1.1
10
UACAAA UU A
GUAU GA A
CGUG CU A
------ -- G
20
dG = 1.2
UA--------- G
CAAA \
GUUU U
CGUGCUGAAAA A
20 10
dG = 1.2
10
UACAAAGUAUU A
UGA A
GCU A
CGU-------- G
20
It's not a false prediction. It's a prediction of no folding and I'd bet money that it's correct.
Date: Fri Apr 24 16:17:11 EDT 2009
Name: kay scheets Email: kay.scheets@okstate.edu URL: http://LSE101-MacG5.cas.okstate.edu Remote Host: LSE101-MacG5.cas.okstate.edu Subject: foldings disappearing within minutes!! Today I folded (individually) 4 short sequences on mfold 3.2 (fixed 37C) and then folded the same sequences on the mfold 2.3/3.4 using 28C. After folding them all, I hit the "View Previous Foldings" link, and successfully saw all 8 foldings listed on the page for this computer. But a few minutes later (I was reexamining figures in the different foldings), when I hit the "View Previous Foldings" link, I got an empty list and the statement that there were no foldings for that computer! A week or so ago I had the same problem, but I think that was done from my PC. I know I can't see foldings from a different computer and that old foldings are eventually deleted, but this seems a bit short! Maybe there's a glitch in your system (or it doesn't like OSU?).
Date: Wed Apr 29 12:10:14 EDT 2009
Name: Whitney Kramer Email: kramwe@gmail.com URL: http:// Remote Host: 241230.dhcp.chop.edu Subject: The effect of methyl groups on DNA hairpin formation Hello- Thank you for a wonderful tool. I am curious to know if methylation of will effect the free energy of hairpin formation for a given sequence. Is you algorithm able to account for base modifications? Whitney
Date: Mon May 11 14:28:13 EDT 2009
Name: Yuk-Ching Tse-Dinh Email: yuk-ching_tse-dinh@nymc.edu URL: http:// Remote Host: 64.118.217.50 Subject: I am very happy to find your program. It is very helpful for our topoisomerase cleavage substrate design. Thank you very much for providing this on the web. 
Date: Fri May 22 05:58:53 EDT 2009
Name: DEEPIKA Email: deep7215@gmail.com URL: http:// Remote Host: gmail.com Subject: hi........... i m student of bioinformatics.plz tell me what should i do for my future??????????? i thought for Msc.bioiofo.Is it right or not? plz tell me. 
Date: Sat May 30 14:32:35 EDT 2009
Name: Kallenbach Email: kallenb@chem-bio.uni-karlsruhe.de URL: http://www.tagesgeldkonto24.info Remote Host: c220037.adsl.hansenet.de Subject: DinaMelt tool The DinaMelt tool helped me a lot with thermal denaturation of a natural DNA segment because some regions of the molecule open at lower temperature than others, giving an experimental denaturation pattern which is specific of the sequence. For very long sequences experiments do not resolve a fine structure and detect the opening of regions that extend over hundreds of base pairs. In this case Ising models, with an appropriate set of parameters, can be successful.
Date: Tue Jun 2 05:26:17 EDT 2009
Name: Michael Bells Email: stud.b.bells@uni-leipzig.de URL: http://www.girokonto-vergleich.net Remote Host: f053096046.adsl.alicedsl.de Subject: UNAFold Software Hello Prof. Zuker, i have some probs installing the software. is there a howto for rookies like me?! thx
Date: Tue Jun 9 05:59:26 EDT 2009
Name: Andi Bernhard Email: mail@andi-bernhard.de URL: http://www.andi-bernhard.de Remote Host: p4FCE9E85.dip0.t-ipconnect.de Subject: mfold Hello Professor Zuker, I tried to install mfold on my OpenSuse Linux but I had some problems with the installation. So I will test UNAFold and hope it works. Thank you for your work. Kind regards
Date: Wed Jun 24 10:17:46 EDT 2009
Name: kay scheets Email: kay.scheets@OKSTATE.Edu URL: http://LSE101-MacG5.cas.okstate.edu Remote Host: LSE101-MacG5.lse.okstate.edu Subject: batch files disappearing On jun22 I submitted some 4 kb batch files and put my email address in for email notification. I never got any notification. When I got back to this site on Jun 23, the system said I had no foldings. I thought I might have gone past the 24 hr limit (if thats what it is), so I resubmitted the batch files, then folded a few shorter sequences immediately. Then when I checked "view previous foldings" the Jun 22 batch foldings were there along with what had been submited Jun 23! I did have to submit one more new batch file late yesterday. Today I don't see anything at "view previous foldings" for that batch file. I did a few immediate foldings to see it the jun 23 folding would appear with today's foldings, and it didn't. Its possible that your email notifications are being filtered out via campus systems, so I need to know what the address would be so I can fix that. But I do not know why yestrday's batch file did not show up today. M. Zuker replies: This reply should be of general interest.
Date: Mon Jul 20 09:36:05 EDT 2009
Name: Michaela Email: stud.michaela.k@bio.uni-erlangen.de URL: Remote Host: 77-23-228-102-dynip.superkabel.de Subject: MFOLD Halo Dr. Michael Zuker, First, I wanna say thank you for providing such an exallent software for students and other users freely. I used Mfold to fold secondary structure of some fragments last year and the figure allowed me to see the nucleotide clearly. But I just tried today but the figure change in another way in which I couldn't see the nucleotide and the number of the length clearly. How can i solve out this problem? Best regards Michaela M. Zuker replies: Very simple. Redraw the structure. The user has full control. You can redraw any structure as many times as you wish. You can rotate the structure through any angle. You can "regularize" angles by forcing all helices to be an integral number of regularization angles from horizontal. You can draw in natural mode (some overlap may occur) or in automatic untangle mode and so on. There are many options. Experiment. 
Date: Wed Jul 29 15:45:32 EDT 2009
Name: KCV Email: vickerskc@nhlbi.nih.gov URL: http:// Remote Host: bldg10-11-58.nhlbi.nih.gov Subject: initial deltaG Is initial deltaG the same thing as minimal free folding energy (MFE) concerning hairpins?
Date: Fri Aug 14 03:43:30 EDT 2009
Name: Lauren Hile Email: watching@i.am URL: Remote Host: cpe.net.cable.rogers.com Subject: Excellent Hi Dr. Zuker, Your software looks great, but is there a visual tutorial or faq for Mfold that I'm missing. I downloaded the v3.1.12 tarball, but I can't seem to find the documentation. M. Zuker replies: Documentation is contained in the 'doc' directory when you open the "tarball" (tar -zvf mfold-3.4.tar.gz). Open 'manual.pdf' or 'manual.ps'. There is even an html version in doc/manual-html. This html version may also be found here. You are urged to download the newer and better UNAFold software that replaces
Date: Thu Aug 27 19:48:45 EDT 2009
Name: Peter Houde Email: phoude@nmsu.edu URL: http://biology-web.nmsu.edu/houde/phoude.htm Remote Host: vert-lab-1.NMSU.Edu Subject: thank you Thank you very much for generously providing this useful tool and service.
Date: Thu Sep 10 17:32:39 EDT 2009
Name: Yang Che Email: vb8add@gmail.com URL: Remote Host: 216.123.211.13 Subject: Thank you so much I was overjoyed to find your program, it is very useful for my substrate design. Thanks alot! 
Date: Mon Sep 21 05:40:52 EDT 2009
Name: Shifra Ben-Dor Email: shifra.ben-dor@weizmann.ac.il URL: http:// Remote Host: wisweb2-out.weizmann.ac.il Subject: which version is the current one on the web server Hi, On the entry page to the server, it says it is version 3.2, but when I get the results on top of the page it says (3.4). Which version is running? I'd like to know to cite it properly. Thanks! Always a pleasure using your server, though I haven't had the opportunity for a while... M. Zuker replies: Sorry about that. Version 3.4 is of mfold is running on the web server. It is the latest. I must correct some out of date information. Thank you for pointing it out to me.
Date: Fri Sep 25 22:09:39 EDT 2009
Name: Greg Matthews Email: gregorymatthews1980@hotmail.com URL: Remote Host: modemcable126.132-59-74.mc.videotron.ca Subject: Thanks Professor Zuker Thanks Professor Zuker! Great site and wonderful support! -Greg
Date: Tue Oct 6 04:16:00 EDT 2009
Name: Dr. Alexander Email: canaryfoot@yahoo.com URL: Remote Host: bas15-montreal02-1279471890.dsl.bell.ca Subject: Thank You! Thank you Dr. Michael Zuker for the wonderful program and site. You do wonderful work and I'm honored in knowing you. M. Zuker replies:I've kept this and the previous message as examples of the kinds of spam that my site receives. The cruder spam is filter automatically. I've erased the URLs that accompanied these two messages.
Date: Thu Oct 22 22:23:07 EDT 2009
Name: Navtej Toor Email: ntoor@ucsd.edu URL: http:// Remote Host: che-uh5234-2.chem.ucsd.edu Subject: Incompatibility with RNAdraw program Hi Dr. Zuker, thank you so much for Mfold! I have used it extensively for my research ever since I was a grad student. However, I have noticed that the .ct files are no longer compatible with RNAdraw. RNAdraw now crashes because the text formatting of the .ct files has changed. I use RNAdraw as a secondary structure viewer quite a bit and was wondering if it is possible to also output .ct files compatible with this program? Thanks a lot, Navtej Toor UC San Diego Dept. of Chemistry and Biochemistry M. Zuker replies:The ct file format for mfold has remained the same for many years, so I do not understand your problem. Our newer UNAFold software that replaces mfold has expanded the ct file format. Two additional columns are added. Our sir_graph structure drawing program from the mfold_util package can handle both the original and the expanded format ct file formats. It is unfortunate that other software developers to not bother to familiarize themselves with the correct syntax of ct files. The same is true for some programs that claim to read "rnaml" output. I have made every effort to support rigid input requirements for poorly written software. For example, the mfold web server offers ct file output in "RnaViz" format. What is the input format for RNAdraw? It seems to me that it would be the same as for RnaViz.
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