Dear Avril.
Thanks for your email.
Hi,
I sent a message to your mailing list but it was rejected.
Please can you put it on your mailing list?
I don’t want to join the mailing list, just to report a bug.
I understand your reluctance to join a mailing list simply to report a bug, so I’ve cc’ed this reply to the list, so others can benefit from the response to your email.
I have been trying to use Jalview to make a muscle alignment, and found a problem with a particular input fasta file (attached).
When I import this into Jalview 2.6 (downloaded to my computer), I find that the alignment made by muscle (called by jalview) is very wierd, it doesn’t have hardly any letters in the two sequences aligned, only gaps, even though they are similar along their lengths (see attached alignment).I’m not sure if this is a muscle problem or a jalview problem, although I used muscle via http://www.ebi.ac.uk/Tools/muscle/index.html and the alignment was fine.
The difference you observed is because different versions of muscle were used to perform the alignment. The default settings for Muscle 3.0 (which is the version used in the original set of Jalview webservices) do not work well for aligning this pair of protein sequences. If you use the JABA Muscle web service (which uses version 3.7 of Muscle) you should find that the two sequences are aligned correctly.
Please note - the JABA services require Java 1.6 in order to run - so you may not be able to see the JABAWS menu entry under the web services menu if you are running Jalview on Java 1.5.
Again, thanks for getting in contact!
Jim.
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J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 [http://www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk)
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