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

Brian Walenz; Liliana Florea

doi:10.1093/bioinformatics/btr285

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

Brian Walenz, Liliana Florea

Research output: Contribution to journal › Article › peer-review

16 Scopus citations

Abstract

Summary: 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.

Original language	English (US)
Article number	btr285
Pages (from-to)	1869-1870
Number of pages	2
Journal	Bioinformatics
Volume	27
Issue number	13
DOIs	https://doi.org/10.1093/bioinformatics/btr285
State	Published - Jul 2011
Externally published	Yes

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btr285

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abstract = "Summary: 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.",

author = "Brian Walenz and Liliana Florea",

note = "Funding Information: Funding: National Institutes of Health (R01-LM006845 to Steven L. Salzberg).",

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doi = "10.1093/bioinformatics/btr285",

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AB - Summary: 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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Sim4db and Leaff: Utilities for fast batch spliced alignment and sequence indexing

Abstract

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