[Jalview-discuss] Changing numbering in alignments

[Engin Ozkan]

Thanks, that does the job. This would be a valuable feature to add.

By the way, copy-and-pasting wasn't necessary: the end position was 
updated immediately when I changed the Name/Description of the sequence.

Engin

On 10/15/10 3:23 AM, Jim Procter 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
>


-- 
Engin Özkan
Post-doctoral Scholar
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
ph: (650)-498-7111