Sim4db and Leaff: utilities for fast batch spliced alignment and sequence indexing | Zendy

Brian P. Walenz | Zendy; Liliana Florea | Zendy

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Sim4db and Leaff: utilities for fast batch spliced alignment and sequence indexing

Author(s) -

Brian P. Walenz,

Liliana Florea

Publication year - 2011

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/btr285

Subject(s) - perl , genome , unix , computer science , sequence (biology) , multiple sequence alignment , sequence alignment , computational biology , search engine indexing , biology , gene , software , genetics , programming language , information retrieval , peptide sequence

The large number of genomes that will be sequenced will need to be annotated with genes and other functional features. Aligning gene sequences from a related species to the target genome is an economical and highly reliable method to identify genes; unfortunately, existing tools have been lacking in sensitivity and speed. A program we reported, sim4cc, was shown to be highly accurate but is limited to comparing one cDNA with one genomic sequence. We present here an optimization of the tool, implemented in the packages sim4db and leaff. The new tool performs batch alignments of cDNA and genomic sequences in a fraction of the time required by its predecessor, and thus is very well suited for genome-wide analyses.

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