Hongyu Zhang1. 1. Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA. me@hongyu.org
Abstract
MOTIVATION: The popular BLAST algorithm is based on a local similarity search strategy, so its high-scoring segment pairs (HSPs) do not have global alignment information. When scientists use BLAST to search for a target protein or DNA sequence in a huge database like the human genome map, the existence of repeated fragments, homologues or pseudogenes in the genome often makes the BLAST result filled with redundant HSPs. Therefore, we need a computational strategy to alleviate this problem. RESULTS: In the gene discovery group of Celera Genomics, I developed a two-step method, i.e. a BLAST step plus an LIS step, to align thousands of cDNA and protein sequences into the human genome map. The LIS step is based on a mature computational algorithm, Longest Increasing Subsequence (LIS) algorithm. The idea is to use the LIS algorithm to find the longest series of consecutive HSPs in the BLAST output. Such a BLAST+LIS strategy can be used as an independent alignment tool or as a complementary tool for other alignment programs like Sim4 and GenWise. It can also work as a general purpose BLAST result processor in all sorts of BLAST searches. Two examples from Celera were shown in this paper.
MOTIVATION: The popular BLAST algorithm is based on a local similarity search strategy, so its high-scoring segment pairs (HSPs) do not have global alignment information. When scientists use BLAST to search for a target protein or DNA sequence in a huge database like the human genome map, the existence of repeated fragments, homologues or pseudogenes in the genome often makes the BLAST result filled with redundant HSPs. Therefore, we need a computational strategy to alleviate this problem. RESULTS: In the gene discovery group of Celera Genomics, I developed a two-step method, i.e. a BLAST step plus an LIS step, to align thousands of cDNA and protein sequences into the human genome map. The LIS step is based on a mature computational algorithm, Longest Increasing Subsequence (LIS) algorithm. The idea is to use the LIS algorithm to find the longest series of consecutive HSPs in the BLAST output. Such a BLAST+LIS strategy can be used as an independent alignment tool or as a complementary tool for other alignment programs like Sim4 and GenWise. It can also work as a general purpose BLAST result processor in all sorts of BLAST searches. Two examples from Celera were shown in this paper.
Authors: L Eichinger; J A Pachebat; G Glöckner; M-A Rajandream; R Sucgang; M Berriman; J Song; R Olsen; K Szafranski; Q Xu; B Tunggal; S Kummerfeld; M Madera; B A Konfortov; F Rivero; A T Bankier; R Lehmann; N Hamlin; R Davies; P Gaudet; P Fey; K Pilcher; G Chen; D Saunders; E Sodergren; P Davis; A Kerhornou; X Nie; N Hall; C Anjard; L Hemphill; N Bason; P Farbrother; B Desany; E Just; T Morio; R Rost; C Churcher; J Cooper; S Haydock; N van Driessche; A Cronin; I Goodhead; D Muzny; T Mourier; A Pain; M Lu; D Harper; R Lindsay; H Hauser; K James; M Quiles; M Madan Babu; T Saito; C Buchrieser; A Wardroper; M Felder; M Thangavelu; D Johnson; A Knights; H Loulseged; K Mungall; K Oliver; C Price; M A Quail; H Urushihara; J Hernandez; E Rabbinowitsch; D Steffen; M Sanders; J Ma; Y Kohara; S Sharp; M Simmonds; S Spiegler; A Tivey; S Sugano; B White; D Walker; J Woodward; T Winckler; Y Tanaka; G Shaulsky; M Schleicher; G Weinstock; A Rosenthal; E C Cox; R L Chisholm; R Gibbs; W F Loomis; M Platzer; R R Kay; J Williams; P H Dear; A A Noegel; B Barrell; A Kuspa Journal: Nature Date: 2005-05-05 Impact factor: 49.962