AlignBucket: a tool to speed up ‘all-against-all’ protein sequence alignments optimizing length constraints | Zendy

Giuseppe Profiti | Zendy; Piero Fariselli | Zendy; Rita Casadio | Zendy

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AlignBucket: a tool to speed up ‘all-against-all’ protein sequence alignments optimizing length constraints

Author(s) -

Giuseppe Profiti,

Piero Fariselli,

Rita Casadio

Publication year - 2015

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/btv451

Subject(s) - computer science , sequence (biology) , annotation , software , partition (number theory) , biological database , bounded function , sequence alignment , data mining , speedup , similarity (geometry) , upload , volume (thermodynamics) , process (computing) , algorithm , bioinformatics , artificial intelligence , mathematics , biology , peptide sequence , parallel computing , gene , mathematical analysis , biochemistry , genetics , physics , combinatorics , quantum mechanics , image (mathematics) , programming language , operating system

The next-generation sequencing era requires reliable, fast and efficient approaches for the accurate annotation of the ever-increasing number of biological sequences and their variations. Transfer of annotation upon similarity search is a standard approach. The procedure of all-against-all protein comparison is a preliminary step of different available methods that annotate sequences based on information already present in databases. Given the actual volume of sequences, methods are necessary to pre-process data to reduce the time of sequence comparison.

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