[Jalview-discuss] Quick Poll: how do you use the sequence ID/start-end numbering ?

Jim Procter jprocter at compbio.dundee.ac.uk
Tue Feb 15 10:34:28 GMT 2011


Joel's recent email prompted me to go an a brief but intense bug hunt,
and one issue that emerged is that Jalview will do 'strange things' if
the sequence's end position is not correct. What I mean by this is that
if you provide an alignment with incorrect numbering, like :
>my sequence/5-9

Jalview will use the start position to number the first residue,
alanine, as 5, and so on, but for certain functions - including the
'find' and jump to residue command in keyboard mode, Jalview will only
highlight/move to the 9th residue - phenylalanine.

The problem only really occurs when the user provided end position is
shorter than the actual number of sequence characters, and I can't
actually think of a case when one might actually want to do this. Can
anyone else ?

Thanks in advance!

ps. Please disregard any cases related to reversed sequences - Jalview
does not currently cope with 3 to 5prime nucleotide or C-N terminal
amino sequences in alignments. In fact, the reason we allow the 'end'
symbol to vary freely was to allow such sequences to be visualised (even
if Jalview then gives completely the wrong sequence positions in
mouseovers, etc).

J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.

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