DocumentCode :
2580907
Title :
ClustDB: A High-Performance Tool for Large Scale Sequence Matching
Author :
Kleffe, Jürgen ; Möller, Friedrich ; Wittig, Burghardt
Author_Institution :
Inst. fur Molekularbiol. und Bioinformatik, Charite Berlin
fYear :
0
fDate :
0-0 0
Firstpage :
196
Lastpage :
200
Abstract :
High throughput sampling of expressed sequence tags (ESTs) has generated huge collections of transcripts that are difficult to compare with each other using existing tools for sequence matching. The major problem is lack of computer memory. We therefore present a new exact and memory efficient algorithm for the simultaneous identification of matching substrings in large sets of sequences. Its application to more than six million human ESTs in Genbank of date 2005-04-06, counting more than 3.3 billion base pairs, takes less than four hours to find all more than seven million clusters of multiple substrings of at least 50 nucleotides in length, say, by using a standard PC with 2 GB of RAM, 2.8 GHz processor speed. The corresponding program ClustDB is able to handle at least eight times more data than VMATCH, the most memory efficient exact software known today. Our program is freely available for academic use
Keywords :
biology computing; data analysis; genetics; sequences; string matching; ClustDB; computer memory; exact algorithm; exact software; expressed sequence tag; high throughput sampling; memory efficient algorithm; sequence matching; substring matching; Bioinformatics; Clustering algorithms; Databases; Genomics; Humans; Large-scale systems; Random access memory; Read-write memory; Sampling methods; Throughput;
fLanguage :
English
Publisher :
ieee
Conference_Titel :
Database and Expert Systems Applications, 2006. DEXA '06. 17th International Workshop on
Conference_Location :
Krakow
ISSN :
1529-4188
Print_ISBN :
0-7695-2641-1
Type :
conf
DOI :
10.1109/DEXA.2006.40
Filename :
1698334
Link To Document :
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