Re: [Seqan-dev] Segments with gaps

["Kehr, Birte" <Birte.Kehr@fu-berlin.de>]

Yes, segment match refinement works with gapped alignments.

However, the current implementation of the Alignment Graph data structure does not store the gaps. Thus, this information is lost after(!) segment match refinement. Vertices of the alignment graph are labelled with sequence segments. It is the edges of the graph that correspond to gapped alignments, but the data structure does not store these alignments as edge labels.

If you give some background on your question, we might be able to help you more specifically.

Birte

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Von: Laécio Freitas Chaves [laeciofreitas@gmail.com]
Gesendet: Mittwoch, 22. Januar 2014 16:26
An: Kehr, Birte
Betreff: Re: [Seqan-dev] Segments with gaps

Ok, Alignment Graph may have vertex corresponds to a gapped sequence segment?

http://trac.seqan.de/wiki/Tutorial/AlignmentRepresentation#AlignmentGraphDataStructure

Segment match refinement works with vertex corresponds to a gapped alignments?

2014/1/22 Kehr, Birte <Birte.Kehr@fu-berlin.de>

Dear Laécio,

I assume that you are asking about the function matchRefinement() in SeqAn.

http://docs.seqan.de/seqan/dev3/?p=matchRefinement

The first parameter of this function is a String of matches. The matches can be of the type Align, which allows gaps. To learn more about the Align type, I recommend the alignment tutorial:

http://trac.seqan.de/wiki/Tutorial/AlignmentRepresentation

So yes, segment match refinement works with gapped alignments.

Birte

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Von: Laécio Freitas Chaves [laeciofreitas@gmail.com]
Gesendet: Dienstag, 21. Januar 2014 18:23
An: SeqAn Development
Betreff: Re: [Seqan-dev] Segments with gaps

For example, in Figure 2 of the article [1] the second and third segment matches could be 

S0: C  -  C 

S1: C G C 

S0: C  -  C 

S1: C Q C 

?

Segment-match refinement works with the segments noted above?

[1]: http://bioinformatics.oxfordjournals.org/content/24/16/i187.full

2014/1/21 Holtgrewe, Manuel <manuel.holtgrewe@fu-berlin.de>

Dear Laecio,

could you make your question more specific and elaborate a bit?

Cheers,

Manuel

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From: Laécio Freitas Chaves [laeciofreitas@gmail.com]
Sent: Tuesday, January 21, 2014 5:05 PM
To: seqan-dev@lists.fu-berlin.de
Subject: [Seqan-dev] Segments with gaps

Hi,

A question: the SeqAn aligns segments matches with gaps?

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