[Bioperl-l] How to align two DNA sequences which are very long?

Tao Zhu tzhu at mail.bnu.edu.cn
Sun Jan 1 07:10:08 EST 2012


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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