[Jalview-discuss] Saving sequence alignments in CLUSTAL format

Charles Ofoegbu (Staff) t.c.n.ofoegbu at dundee.ac.uk
Fri Jan 8 16:31:09 GMT 2016


Dear Linda,

I can confirm that this is a bug in Jalview's Clustal parser, and I’ve filed a bug report about it here<http://issues.jalview.org/browse/JAL-1991>.

This bug should be very quick to fix and would hopefully be resolved in the development version<http://www.jalview.org/builds/develop/webstart/jalview.jnlp> by next week.

Thanks and regards,
Charles



Ofoegbu Tochukwu Charles
Jalview Visual Analytics Developer/Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
Skype: cofoegbu
www.jalview.org<http://www.jalview.org/>
www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk/>​











On 8 Jan 2016, at 03:52 pm, Linda Kazandjian <lindak84 at gmail.com<mailto:lindak84 at gmail.com>> wrote:

Dear Jalview team,

We have encountered an issue in the way how MSAs are saved using the CLUSTAL format under specific conditions: when the length of the MSA (no matter if DNA or protein sequences) is exactly a multiple of 60 (e.g.: 60 nucleotides, 120 nucleotides, 180…) the resulting CLUSTAL file has a superfluous final section where only the sample ID list is reported.

This, per se, is not a problem since Jalview can re-open this file without issues, but it gets problematic if the file has to be uploaded in the program ClustalX. In this case ClustalX creates a 60-nt or 60-aa sequence repetition at the end of each sample.

This problem can be avoided by first opening the CLUSTAL file with a text editor, removing the last section of sample IDs, saving the file again and finally opening it in ClustalX; but it already occurred to us to forget checking this out and ending up with incorrect alignments.

I realize that this is a “cross-program” problem, but since we have always been very impressed by your quick reaction times I was wondering if you would be able to fix this issue from your side…unless fixing it has negative consequences for other users, of course!

Thank you for your support,

Linda
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