Re: [Seqan-dev] align_myer algorithm in seqan/align/align_myer

From: "Holtgrewe, Manuel" <manuel.holtgrewe@fu-berlin.de>
To: SeqAn Development <seqan-dev@lists.fu-berlin.de>
Date: Thu, 28 Jul 2011 12:41:09 +0200
Acceptlanguage: en-US, de-DE
Reply-to: SeqAn Development <seqan-dev@lists.fu-berlin.de>
Subject: Re: [Seqan-dev] align_myer algorithm in seqan/align/align_myer

Am 28.07.2011 um 04:12 schrieb Lingjie Weng:

> Hi,
> 
> I was wondering if you have combined Ukkonen algorithm into the 
> align_myers algorithm in Seqan_Release_1.3/seqan/align/align_myers.h.  
> If yes, can you explain how you update the "last active cell"?

No, it's implemented in the Finder MyersUkkonen, though.

> In addition, do you have a banded MyersUkkneon algorithm for global 
> alignment. The one I found under 
> Seqan_Release_1.3/seqan/find/find_myers_ukkonen is not applicable to 
> global alignment.

Yes, you are right. The banded Myers Ukkonen not applicable to global alignments.

You can try to use the banded globalAlignment() algorithm (Gotoh/NW).

Bests,
Manuel

<-- thread -->

<-- date -->

Follow-Ups:
- Re: [Seqan-dev] align_myer algorithm in seqan/align/align_myer
  - From: Lingjie Weng <wengl@uci.edu>

References:
- [Seqan-dev] Time complexity of posGlobalize
  - From: John Reid <j.reid@mail.cryst.bbk.ac.uk>
- Re: [Seqan-dev] Time complexity of posGlobalize
  - From: "Weese, David" <weese@campus.fu-berlin.de>
- Re: [Seqan-dev] Time complexity of posGlobalize
  - From: John Reid <j.reid@mail.cryst.bbk.ac.uk>
- Re: [Seqan-dev] Time complexity of posGlobalize
  - From: John Reid <j.reid@mail.cryst.bbk.ac.uk>
- Re: [Seqan-dev] Time complexity of posGlobalize
  - From: "Weese, David" <weese@campus.fu-berlin.de>
- [Seqan-dev] align_myer algorithm in seqan/align/align_myer
  - From: Lingjie Weng <wengl@uci.edu>

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