Re: [Seqan-dev] Asymmetric Scoring of Insertions / Deletions in Alignments
- From: Rahn, René <rene.maerker@fu-berlin.de>
- To: SeqAn Development <seqan-dev@lists.fu-berlin.de>
- Date: Wed, 03 Jun 2015 17:21:18 +0200
- Reply-to: SeqAn Development <seqan-dev@lists.fu-berlin.de>
- Subject: Re: [Seqan-dev] Asymmetric Scoring of Insertions / Deletions in Alignments
Hi Brett,
this is possible with the BiAffine Score specification.
However this was so far only used in the JournaledStringSet module which is still under development.
You can access it by simply including <seqan/journaled_set/score_biaffine.h>
You can use the setter and getter functions:
setScore/score
setScoreMismatch/scoreMismatch
setScoreGapOpenVertical/scoreGapOpenVertical
setScoreGapOpenHorizontal/scoreGapOpenHorizontal
and of course the standard setGap interfaces.
Apart from this, the entire align engine for the standard DP algorithms works with different gap penalties for insertions/deletions.
Cheers,
René
---
René Rahn
Ph.D. Student
--------------------------------
Institute of Computer Science
Algorithmic Bioinformatics (ABI)
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Freie Universität Berlin
Takustraße 9
14195 Berlin
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