Incorrect feature mapping on gapped sequencs

When loading up a features file generated by a script onto a fasta nucleotide sequence containing gaps, the features are not shown in the correct place.

In this file the features have been labelled with the correct ungapped position in the description, the feature position given is the position in the gapped sequence.

Loading these up an example is at position ~8290 where the feature is shown starting at 8289 instead of 8279 . I’ve reproduced this on Win 7. The original discoverer was using Mac OS X.

Attached a sequence and feature file.

…d

m_meles.fasta (18.4 KB)

features_spei.txt (543 Bytes)

Hello David,

I have loaded up your example and what I see is:

  • columns 8289-8295 show feature located on bases 8093-8099 of the sequence (positions confirmed in the status bar)

  • columns 8475-8481 show feature located on bases 8279-8285 " " " " " " "

‘Remove all gaps’ and the feature positions and column positions are the same.

This all looks ok to me. The feature positions are always numbered as per the sequence (base/residue numbering), not the alignment columns.

I hope that clarifies things - if not, or if you are seeing anything different, please let us know!

Regards,

Mungo

The University of Dundee is a registered Scottish Charity, No: SC015096

···

Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
www.jalview.org
www.compbio.dundee.ac.uk


From: jalview-discuss-bounces@jalview.org jalview-discuss-bounces@jalview.org on behalf of David Martin (Staff) d.m.a.martin@dundee.ac.uk
Sent: 25 February 2016 13:37
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] Incorrect feature mapping on gapped sequencs

When loading up a features file generated by a script onto a fasta nucleotide sequence containing gaps, the features are not shown in the correct place.

In this file the features have been labelled with the correct ungapped position in the description, the feature position given is the position in the gapped sequence.

Loading these up an example is at position ~8290 where the feature is shown starting at 8289 instead of 8279 . I’ve reproduced this on Win 7. The original discoverer was using Mac OS X.

Attached a sequence and feature file.

…d

The University of Dundee is a registered Scottish Charity, No: SC015096

When loading up a features file generated by a script onto a fasta nucleotide sequence containing gaps, the features are not shown in the correct place.

In this file the features have been labelled with the correct ungapped position in the description, the feature position given is the position in the gapped sequence.

Loading these up an example is at position ~8290 where the feature is shown starting at 8289 instead of 8279 . I’ve reproduced this on Win 7. The original discoverer was using Mac OS X.

Attached a sequence and feature file.

…d

Hello Peter - you might find the Jalview training video on this topic helpful:
https://www.youtube.com/watch?v=b0M0eQf6qFY

···

On 25/02/2016 13:57, Peter Felker wrote:

Hello
I forgot how to color amino acids of the same identity. Would you please
refresh me on that
Thank you
Peter

Sent from my iPhone

On Feb 25, 2016, at 5:37 AM, "David Martin (Staff)" > <d.m.a.martin@dundee.ac.uk <mailto:d.m.a.martin@dundee.ac.uk>> wrote:

> When loading up a features file generated by a script onto a fasta
> nucleotide sequence containing gaps, the features are not shown in the
> correct place.
>
>
>
> In this file the features have been labelled with the correct ungapped
> position in the description, the feature position given is the
> position in the gapped sequence.
>
> Loading these up an example is at position ~8290 where the feature is
> shown starting at 8289 instead of 8279 . I’ve reproduced this on Win
> 7. The original discoverer was using Mac OS X.
>
>
>
> Attached a sequence and feature file.
>
>
>
> ..d
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
> <m_meles.fasta>
> <features_spei.txt>
> _______________________________________________
> Jalview-discuss mailing list
> Jalview-discuss@jalview.org <mailto:Jalview-discuss@jalview.org>
> http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

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