Re: [Seqan-dev] Segments with gaps

[Laécio Freitas Chaves <laeciofreitas@gmail.com>]

In case of segments of MuMmer, how the segment matches are scored?

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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