./wip/GSAlign, Ultra-fast intra-species sequence alignment

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Branch: CURRENT, Version: 1.0.22, Package name: GSAlign-1.0.22, Maintainer: pkgsrc-users

GSAlign: an ultra-fast sequence alignment algorithm for intra-species
genome comparison

Personal genomics and comparative genomics are two fields that are
more and more important in clinical practices and genome
researches. Both fields require sequence alignment to discover
sequence conservation and structural variation. Though many methods
have been developed to handle genome sequence alignment, some are
designed for small genome comparison while some are not efficient for
large genome comparison. Here, we present GSAlign to handle large
genome comparison efficiently. GSAlign includes three unique features:
1) it is the first attempt to use Burrows-Wheeler Transform on genome
sequence alignment; 2) it supports parallel computing; 3) it adopts a
divide-and-conquer strategy to separate a query sequence into regions
that are easy to align and regions that require gapped alignment. With
all these features, we demonstrated GSAlign is very efficient and
sensitive in finding both the exact matches and differences between
two genome sequences and it is much faster than existing
state-of-the-art methods.

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