Fast and Sensitive Algorithm for Aligning ESTs to Human Genome

There is a pressing need to align growing set of expressed sequence tags (ESTs) to newly sequenced human genome. The problem is, however, complicated by the exon/intron structure of eucaryotic genes, misread nucleotides in ESTs, and millions of repeptive sequences in genomic sequences. Indeed, to solve this, algorithms that use dynamic programming have been proposed, but in reality, these algorithms require an enormous amount of processing time. In an effort to improve the computational efficiency of these classical DP algorithms, we develop software that fully utilizes the lookup-table for allowing the efficient detection of the start- and endpoints of an EST within a given DNA sequence, and subsequently, the prompt identification of exons and introns. In addition, high sensitivity and accuracy must be achieved by calculating locations of all spliced sites correctly for more ESTs while retaining high computational efficiency. This goal is hard to accomplish in practice, owing to ...

• Type: Conference
• Year: 2002
• Where: CSB
• Authors: Jun Ogasawara, Shinichi Morishita
• Keywords: Bioinformatics, Computational Efficiency, CSB 2002, Expressed Sequence Tags, Repeptive Sequences