[Jalview-discuss] Changing numbering in alignments

[Ackers, Jared (DEWN)]

If you are changing options around the numbering, it would be nice to have the choice not to have numbers at all.  In our application we have custom labels for thousands of sequences, and I end up having to strip the forward slash and numbers out of the labels with other programs later.  

Thanks,

Jared

-----Original Message-----
From: jalview-discuss-bounces at jalview.org [mailto:jalview-discuss-bounces at jalview.org] On Behalf Of Engin Ozkan
Sent: Friday, October 15, 2010 4:48 PM
To: jalview-discuss at jalview.org
Subject: Re: [Jalview-discuss] Changing numbering in alignments


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

_______________________________________________
Jalview-discuss mailing list
Jalview-discuss at jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

______________________________________________________________________
CAUTION: This message was sent via the Public Internet and its authenticity cannot be guaranteed.

This message sent from Smiths Detection, a division of Smiths Group.

PROPRIETARY: This e-mail contains proprietary information some or all of which may be legally privileged. It is intended for the recipient only. If an addressing or transmission error has misdirected this e-mail, please notify the authority by replying to this e-mail. If you are not the intended recipient you must not use, disclose, distribute, copy, print, or rely on this e-mail.