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

Bioinformatics. 2011 Jul 1;27(13):1869-70. doi: 10.1093/bioinformatics/btr285. Epub 2011 May 6.


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.

Availability: Sim4db and leaff are written in C, C++ and Perl for Linux and other Unix platforms. Source code is distributed free of charge from


Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Base Sequence
  • Biological Evolution
  • DNA, Complementary / genetics
  • Genome
  • Humans
  • RNA Splicing
  • Sequence Alignment / methods*
  • Software*
  • Vertebrates / genetics


  • DNA, Complementary