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

Andrew Perry ajperry at pansapiens.com
Thu Feb 17 00:12:03 GMT 2011


On Tue, Feb 15, 2011 at 9:34 PM, Jim Procter
<jprocter at compbio.dundee.ac.uk>wrote:

>
> Hi.
>
> 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
> ASDQFNSQNWSTQ
>
> 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!
> Jim.
>
>
Hi Jim,

I think in this case the potential for confusion outweighs any utility in
being able to restrict the search region for 'Find' by using the user
defined start and end positions.

My vote would be to make 'Find' work on the full length sequence and ignore
the /1-X numbering.

I've noticed that if you select a region within an alignment (ie by dragging
the mouse) then 'Find' is restricted to this region - that functionality
should be enough in the case where someone wanted to search within a defined
region.

Cheers,

Andrew Perry

Postdoctoral Fellow
Whisstock Lab
Department of Biochemistry and Molecular Biology
Monash University, Clayton Campus, PO Box 13d, VIC, 3800, Australia.
Mobile: +61 409 808 529
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