A Fast and Sensitive Algorithm for Aligning ESTs to the Human Genome

Introduction The Human Genome Project is an international collaboration, designed to investigate the genetic complexity of humans. Initially, the roughly three billion nucleotides of the human genome were elucidated (Celera Genomics , International Human Genome Sequencing Consortium ). The next step involves interpreting the encoded sequences. In order to identify the coding regions, i.e., regions containing exons and introns, of any given DNA sequence, many ESTs must be aligned with genomic DNA to reveal these complex structures, while verifying alternative splicing transcripts. The alignment of full-length cDNAs gives clues to regulatory elements in the upstream regions. Furthermore, the annotation of the upstream regions using Transfac data identifies the candidates of cis-elements. The alignment of both sequences associated with expression patterns and sequences from dbSNP with the identified locations of SNPs near the gene, enables more detailed functional 2 Jun Ogasawara