Bridges: a tool for identifying local similarities in long sequences | Zendy

Alexey S. Kondrashov | Zendy; Raquel Assis | Zendy

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Bridges: a tool for identifying local similarities in long sequences

Author(s) -

Alexey S. Kondrashov,

Raquel Assis

Publication year - 2010

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btq320

Subject(s) - computer science , documentation , heuristic , code (set theory) , word (group theory) , source code , sequence (biology) , scale (ratio) , sensitivity (control systems) , software , data mining , information retrieval , artificial intelligence , programming language , linguistics , philosophy , physics , set (abstract data type) , quantum mechanics , electronic engineering , biology , engineering , genetics

Bridges is a heuristic search tool that uses short word matches to rapidly identify local similarities between sequences. It consists of three stages: filtering input sequences, identifying local similarities and post-processing local similarities. As input sequence data are released from memory after the filtering stage, genome-scale datasets can be efficiently compared in a single run. Bridges also includes 20 parameters, which enable the user to dictate the sensitivity and specificity of a search.

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