Re: [Seqan-dev] match number of globalalignment
- From: "Weese, David" <weese@campus.fu-berlin.de>
- To: SeqAn Development <seqan-dev@lists.fu-berlin.de>
- Date: Fri, 13 Jan 2012 20:24:12 +0100
- Acceptlanguage: de-DE
- Reply-to: SeqAn Development <seqan-dev@lists.fu-berlin.de>
- Subject: Re: [Seqan-dev] match number of globalalignment
Hi, You can iterate with two iterators it1, it2 simultaneously over the two rows of the align object, see Task 1 of http://trac.seqan.de/wiki/Tutorial/Alignments. A match occurs whenever both isGap(it1) and isGap(it2) are false. Simply count them. Regards, David -- David Weese weese@inf.fu-berlin.de Freie Universität Berlin http://www.inf.fu-berlin.de/ Institut für Informatik Phone: +49 30 838 75246 Takustraße 9 Algorithmic Bioinformatics 14195 Berlin Room 021 Am 13.01.2012 um 20:11 schrieb Beifang Niu: > Hi David, > > One example for match number is the following: > > If I got the alignment using global alignment, the match number is 5. > > AACCGT > | | | | | > AATCGT > > I just can get the alignment using globalalignment but how can I get the match number of base pairs ? > > thanks, > Beifang. >
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- From: Beifang Niu <neilniu.cn@gmail.com>
- Re: [Seqan-dev] match number of globalalignment
- From: "Weese, David" <weese@campus.fu-berlin.de>
- [Seqan-dev] match number of globalalignment
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