[Jalview-discuss] Changing numbering in alignments
Donado, Carlos A
carlosdonado at WPI.EDU
Fri Oct 15 20:26:09 BST 2010
Sent from my iPhoneq
On Oct 15, 2010, at 6:23 AM, "Jim Procter" <jprocter at compbio.dundee.ac.uk> wrote:
> Dear Engin,
> On 15/10/2010 06:28, Engin Ozkan wrote:
>> I am wondering if it is possible to change the sequence numbering of
>> sequences in any multiple sequence alignment. For example, within an MSA
>> with 100-residue sequences, can I change them to designate residues as
>> 4-104, 510-610, etc. Sequences are not from a database (like a swissprot
>> entry), and I don't see this mentioned in the documentation.
> You're quite right - there isn't a documented option to modify the
> start/end numbering of the sequence, which is a small but significant
> You can actually change the start/end numbering given for a sequence
> using the 'Edit Name/Description' dialog box. Simply add the new
> numbering to the sequence ID using the standard '/start-end' syntax, and
> it will be updated in the alignment.
> However - be warned, there is no error checking for the start/end
> actually corresponding to the length of your sequences (which is
> probably why this was not documented!). I just played with this myself
> to check its behaviour when there is annotation on the alignment, and
> found that there are some surprising 'emergent features' that will have
> to be dealt with in a future release.
> For the moment - should you have to edit the start/end position for
> sequences, make absolutely sure that the start position is correct.
> Then, once you've modified all the sequences you need to, select all the
> sequences in the alignment and copy and paste them to a new alignment
> window - Jalview will then update all the end positions according to the
> number of non-gap symbols actually in each sequence.
> Best of luck! ;)
> ps. I've created a new feature request regarding start/end editing here:
> 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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