The SSAHA trace server

Author

Ning, Zemin ; Spooner, William ; Spargo, Adam ; Leonard, Steven ; Rae, Mark ; Cox, Antony

Author_Institution

Wellcome Trust Sanger Inst., Cambridge, UK

fYear

2004

fDate

16-19 Aug. 2004

Firstpage

544

Lastpage

545

Abstract

We present a client/server database system with the potential to make all DNA sequences searchable. The database estimated to be approximately 200 Gbps, contains various types of sequences, including WGS and clone reads, draft assemblies, finished sequences, refSeq etc. The search engine will be SSAHA2, a package combined SSAHA (sequence search and alignment by hashing algorithm) with cross_match. Matching seeds of a few kmer words are detected by the SSAHA algorithm. Both query and subject sequences are cut off according to the locations of the matching seeds and then passed to cross_match for full alignment. We aim to develop a platform-independent client/server system which can provide a near real-time (under 10 seconds) search service for a clustered database.

Keywords

DNA; biology computing; client-server systems; file organisation; molecular biophysics; search engines; DNA sequences; SSAHA trace server; SSAHA2; WGS sequences; client/server database system; clone reads; clustered database; cross_match; draft assemblies; finished sequences; hashing algorithm; matching seeds; query sequences; refSeq sequences; search engine; sequence alignment; sequence search; subject sequences; Assembly; Bioinformatics; Cloning; DNA; Database systems; Encoding; Genomics; Packaging; Search engines; Sequences;

fLanguage

English

Publisher

ieee

Conference_Titel

Computational Systems Bioinformatics Conference, 2004. CSB 2004. Proceedings. 2004 IEEE

Print_ISBN

0-7695-2194-0

Type

conf

DOI

10.1109/CSB.2004.1332490

Filename

1332490