[Bioperl-l] Bioperl-l Digest, Vol 105, Issue 1

[Michael Coyne]

You can try MUSCLE (see http://www.drive5.com/muscle).

On Sun, Jan 1, 2012 at 12:00 PM, <bioperl-l-request at lists.open-bio.org>wrote:

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> Today's Topics:
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>   1.  How to align two DNA sequences which are very long? (Tao Zhu)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 01 Jan 2012 20:10:08 +0800
> From: Tao Zhu <tzhu at mail.bnu.edu.cn>
> Subject: [Bioperl-l] How to align two DNA sequences which are very
>        long?
> To: BioPerl <bioperl-l at lists.open-bio.org>
> Message-ID: <4F004D20.3030009 at mail.bnu.edu.cn>
> Content-Type: text/plain; charset=UTF-8
>
> Hello, everyone
>
> This problem may not relate to BioPerl directly, but relate to
> bioinformatics.
>
> ClustalW is a good method to do multiple sequences alignment. However,
> if sequence is long, it would become extremely slow.
>
> I want to align a pair of mouse-rat ortholog, ENSMUSG00000000131 and
> ENSRNOG00000016722, which is 98787 bp and 89851 bp, respectively. I took
> almost 1.5 hours to finish alignment using clustalw!
>
> Is there a faster way to align two long DNA sequences? I want global
> alignment.
>
>
> --
> Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
> 100875, China
> Email: tzhu at mail.bnu.edu.cn
>
>
>
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> End of Bioperl-l Digest, Vol 105, Issue 1
> *****************************************
>