title: Sim4db and Leaff: utilities for fast batch spliced alignment and sequence indexing.
abstract: 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.
  
  
  BACKGROUND
  Sim4db and leaff are written in C, C++ and Perl for Linux and other Unix platforms. Source code is distributed free of charge from http://sourceforge.net/projects/kmer/.
  
  
  BACKGROUND
  florea@umiacs.umd.edu
authors.affiliation: The J. Craig Venter Institute, Rockville, MD 20850, USA.
authors.forename: Brian
authors.initials: B
authors.lastname: Walenz
authors.forename: Liliana
authors.initials: L
authors.lastname: Florea
mesh_terms: D000818:Animals; D001483:Base Sequence; D005075:Biological Evolution; D018076:DNA, Complementary / Q000235:genetics; D016678:Genome; D006801:Humans; D012326:RNA Splicing; D016415:Sequence Alignment / Q000379:methods*; D012984:Software; D014714:Vertebrates / Q000235:genetics
chemical_list: D018076:DNA, Complementary