GAST, a Genomic Alignment Search Tool

Alignment to a genomic sequence is a common task in modern bioinformatics. By improving the methods used, significant amount of time and resources can be saved. We have developed a new genomic alignment search tool, called GAST, for sequences of at least 160 nt. GAST is many times faster than commonly used alignment tools BLAT and Mega BLAST. As the sizes of query sequences and the database increase, the advantage grows. This paper describes the principles of GAST and reports a comparison of GAST with BLAT and Mega BLAST. The effects the query sequence length and the number of queries have on run times were studied using the full human genome and the chromosome 1 of human genome separately. Additionally, the error tolerance and behaviour of GAST when handling sequences with lower similarity to a database was studied. Lastly, we compared the quality of exon mappings produced by the three tools and the genomic