residue numbering changes

Jalview Discussion
1

Hello,

I noticed that after I modify and save sequence alignment in Jalview it changes residue numbering so that the first residue of all sequences becomes number 1. Is there a way to preserve the original residue numbering?

Thanks,
Vladimir

2

Hi Vladimir,

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On 08/06/2011 07:31, Vladimir Yarov-Yarovoy wrote:

I noticed that after I modify and save sequence alignment in Jalview it
changes residue numbering so that the first residue of all sequences
becomes number 1. Is there a way to preserve the original residue
numbering?

Normally Jalview does preserve the numbering - so perhaps it did not recognise the original residue numbering in your input sequences. Can you send me an example to demonstrate this ?

Jim.

3

Thanks very much for this. You have indeed uncovered a tiny, but particularly ancient bug, which is now fixed!

The fix is available in the development version of jalview (bug JAL-847), and will also be included in the version 2.7 release.

Jim.

···

On 22/07/28164 20:59, Vladimir Yarov-Yarovoy wrote:

Sure - please see the attached example. The first .msf file contains the original full sequences and correct numbering and the second .msf file was created by Jalview after I deleted certain N- and C-terminal regions and only saved the middle region of the alignment. Note that all the sequences start from 1 in the second .msf file, although they should start from numbers shown in the third (.png) file.