Using multiple alignments to improve seeded local alignment algorithms. Export

@article{citeulike:525659, abstract = {Multiple alignments among genomes are becoming increasingly prevalent. This trend motivates the development of tools for efficient homology search between a query sequence and a database of multiple alignments. In this paper, we present an algorithm that uses the information implicit in a multiple alignment to dynamically build an index that is weighted most heavily towards the promising regions of the multiple alignment. We have implemented Typhon, a local alignment tool that incorporates our indexing algorithm, which our test results show to be more sensitive than algorithms that index only a sequence. This suggests that when applied on a whole-genome scale, Typhon should provide improved homology searches in time comparable to existing algorithms.}, address = {Department of Computer Science, Stanford University, Stanford, CA 94304, USA. flannick@cs.stanford.edu}, author = {Flannick, J. and Batzoglou, S.}, citeulike-article-id = {525659}, citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/16100379}, citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=16100379}, issn = {1362-4962}, journal = {Nucleic Acids Res}, keywords = {nsfbatz}, number = {14}, pages = {4563--4577}, posted-at = {2006-03-01 17:59:03}, priority = {2}, title = {Using multiple alignments to improve seeded local alignment algorithms.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/16100379}, volume = {33}, year = {2005} }

TY - JOUR ID - citeulike:525659 L3 - citeulike-article-id:525659 N2 - Multiple alignments among genomes are becoming increasingly prevalent. This trend motivates the development of tools for efficient homology search between a query sequence and a database of multiple alignments. In this paper, we present an algorithm that uses the information implicit in a multiple alignment to dynamically build an index that is weighted most heavily towards the promising regions of the multiple alignment. We have implemented Typhon, a local alignment tool that incorporates our indexing algorithm, which our test results show to be more sensitive than algorithms that index only a sequence. This suggests that when applied on a whole-genome scale, Typhon should provide improved homology searches in time comparable to existing algorithms. IS - 14 JF - Nucleic Acids Res SN - 1362-4962 AD - Department of Computer Science, Stanford University, Stanford, CA 94304, USA. flannick@cs.stanford.edu EP - 4577 TI - Using multiple alignments to improve seeded local alignment algorithms. VL - 33 SP - 4563 KW - nsfbatz AU - Flannick, J AU - Batzoglou, S PY - 2005/// UR - http://view.ncbi.nlm.nih.gov/pubmed/16100379 ER -