wip/GSAlign 1.0.22 NetBSD

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.