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

Brian Walenz, Liliana D Florea

Research output: Contribution to journalArticle

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 languageEnglish (US)
Article numberbtr285
Pages (from-to)1869-1870
Number of pages2
JournalBioinformatics
Volume27
Issue number13
DOIs
StatePublished - Jul 2011
Externally publishedYes

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Sequence Alignment
Indexing
Batch
Genome
Alignment
Genes
CDNA
Gene
Genomics
Complementary DNA
Target
Optimization

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

Sim4db and Leaff : Utilities for fast batch spliced alignment and sequence indexing. / Walenz, Brian; Florea, Liliana D.

In: Bioinformatics, Vol. 27, No. 13, btr285, 07.2011, p. 1869-1870.

Research output: Contribution to journalArticle

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