[Jalview-discuss] Changing numbering in alignments

[Donado, Carlos A]

 Ommom

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 
> oversight.
> 
> 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! ;)
> Jim.
> 
> ps. I've created a new feature request regarding start/end editing here: 
> http://issues.jalview.org/browse/JAL-680
> 
> -- 
> -------------------------------------------------------------------
> 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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