From taylorjs at uvic.ca Fri Feb 15 04:09:27 2008 From: taylorjs at uvic.ca (taylorjs) Date: Fri Feb 15 04:13:42 2008 Subject: [Jalview-discuss] rev_complement Message-ID: <62328.142.104.193.193.1203048567.squirrel@wm3.uvic.ca> Hello again, Is it possible to reverse complement nucleotide sequences? If not, this, along with the toggle translation option mentioned in my last post, would be very helpful. Also, please let me know if this is not the best forum for making such requests. Thanks, John From jimp at compbio.dundee.ac.uk Fri Feb 15 11:01:38 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Fri Feb 15 11:02:28 2008 Subject: [Jalview-discuss] rev_complement In-Reply-To: <62328.142.104.193.193.1203048567.squirrel@wm3.uvic.ca> References: <62328.142.104.193.193.1203048567.squirrel@wm3.uvic.ca> Message-ID: <47B57112.9070307@compbio.dundee.ac.uk> Hi John. taylorjs wrote: > Is it possible to reverse complement nucleotide sequences? nope - a basic facility would be quite easy to implement - although I'd ideally also like some kind of mapping to be preserved between the original sequence and the complement. This would be in the same way that translated dna sequences retain a mapping between them and their protein products - a feature which is being introduced in Jalview 2.4. > along with the toggle translation option mentioned in my last post, would > be very helpful. Also, please let me know if this is not the best forum > for making such requests. this is the right forum - but I'm not sure if you've posted before (although I did recover your email from a few years ago!). thanks for the feature request. Jim From peter_felker at hotmail.com Fri Feb 15 14:52:52 2008 From: peter_felker at hotmail.com (Peter Felker) Date: Fri Feb 15 14:53:00 2008 Subject: [Jalview-discuss] rev_complement In-Reply-To: <47B57112.9070307@compbio.dundee.ac.uk> References: <62328.142.104.193.193.1203048567.squirrel@wm3.uvic.ca> <47B57112.9070307@compbio.dundee.ac.uk> Message-ID: Good morning I generally do the reverse and complements on ChromasPro which has a free version and a very modestly priced version (about $150). It is also very good for checking the chromatograms of several aligned files Peter Peter Felker D'Arrigo Bros. Co 831 235 2847 (Cell) Address for: US Mail and INTERNATIONAL EMS P. O. Box 850 Salinas, CA 93902 Address for: FEDEX, UPS, DHL delivery: 20911 Harris Road Spreckels, CA 93962 831 235 2847 (cell) Peter_Felker@hotmail.com > Date: Fri, 15 Feb 2008 11:01:38 +0000 > From: jimp@compbio.dundee.ac.uk > To: jalview-discuss@jalview.org > Subject: Re: [Jalview-discuss] rev_complement > > Hi John. > > taylorjs wrote: > > Is it possible to reverse complement nucleotide sequences? > nope - a basic facility would be quite easy to implement - although I'd > ideally also like some kind of mapping to be preserved between the > original sequence and the complement. This would be in the same way that > translated dna sequences retain a mapping between them and their protein > products - a feature which is being introduced in Jalview 2.4. > > > along with the toggle translation option mentioned in my last post, would > > be very helpful. Also, please let me know if this is not the best forum > > for making such requests. > this is the right forum - but I'm not sure if you've posted before > (although I did recover your email from a few years ago!). > > thanks for the feature request. > Jim > > _______________________________________________ > Jalview-discuss mailing list > Jalview-discuss@jalview.org > http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.jalview.org/pipermail/jalview-discuss/attachments/20080215/72075d96/attachment.htm From taylorjs at uvic.ca Fri Feb 15 17:44:17 2008 From: taylorjs at uvic.ca (John Taylor) Date: Fri Feb 15 17:44:22 2008 Subject: [Jalview-discuss] rev_complement Message-ID: <1203097457.3945.437.camel@lynch> Hi, It looks like my first message was sent before I was added to the list (so it didn't arrive). I asked about a toggle translation option in addition to the reverse complement. These are tools I use a lot in BioEdit. They are very handy for research and teaching. Toggle translate allows one to get sequences in the proper reading frame. It also allows one to switch to amino acids for alignment and then back so you end up with a codon alignment. The reverse complement option is also handy. My aim is to convert my lab to Linux. BioEdit is the main thing holding us back (it's only available for Windows). When might we expect Jalview 2.4? Thanks very much, John From jimp at compbio.dundee.ac.uk Tue Feb 19 15:45:19 2008 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Tue Feb 19 15:45:34 2008 Subject: [Jalview-discuss] rev_complement In-Reply-To: <1203097457.3945.437.camel@lynch> References: <1203097457.3945.437.camel@lynch> Message-ID: <47BAF98F.305@compbio.dundee.ac.uk> Thanks for posting to the list again, John. John Taylor wrote: > (so it didn't arrive). I asked about a toggle translation option in > addition to the reverse complement. These are tools I use a lot in > BioEdit. They are very handy for research and teaching. Toggle I can imagine. I think BioEdit still has a lot of fans out there because it's got some really practical features. > translate allows one to get sequences in the proper reading frame. It > also allows one to switch to amino acids for alignment and then back so > you end up with a codon alignment. Does it preserve the variable sites in the third position from the original DNA at the end of all this ? A few months ago there was a feature request concerning something like this, but in that case the idea would be to either have one view which showed the codon alignment, and the other would be the corresponding protein alignment. Scrolling would be tied between both alignment views, so moving the focus in one would also move the other. I'm afraid that kind of manipulation is not yet implemented either, but I'm just trying to get an idea of what would be most useful to everyone. The back-translation function is really the most significant missing feature in Jalview at the moment. If the sequence is in Uniprot and has an EMBL cross reference then it can retrieve that sequence and propagate annotation from the protein back onto it, but not much more. Going from DNA to protein is better supported (ie an aligned set of coding regions are properly translated to an aligned set of proteins), but for a protein alignment there's curently no way of reconstructing the aligned cDNA from it. All the basic mechanisms are available to do this, but we have to find (someone's) time to actually write the routine to do it. The reverse complement option is > also handy. My aim is to convert my lab to Linux. BioEdit is the main > thing holding us back (it's only available for Windows). Wine may be the only way forward at the moment :( perhaps this'll change in a few months, though. > When might we expect Jalview 2.4? There is a paper being drafted at the moment, and so the official release of 2.4 has been delayed until this is complete. However, you can get at a webstart version of the application from here: http://www.compbio.dundee.ac.uk/~ws-dev1/jalview/release/webstart/jalview.jnlp Jim.