title: Exon discovery by genomic sequence alignment.
abstract: BACKGROUND
  During evolution, functional regions in genomic sequences tend to be more highly conserved than randomly mutating 'junk DNA' so local sequence similarity often indicates biological functionality. This fact can be used to identify functional elements in large eukaryotic DNA sequences by cross-species sequence comparison. In recent years, several gene-prediction methods have been proposed that work by comparing anonymous genomic sequences, for example from human and mouse. The main advantage of these methods is that they are based on simple and generally applicable measures of (local) sequence similarity; unlike standard gene-finding approaches they do not depend on species-specific training data or on the presence of cognate genes in data bases. As all comparative sequence-analysis methods, the new comparative gene-finding approaches critically rely on the quality of the underlying sequence alignments.
  
  
  RESULTS
  Herein, we describe a new implementation of the sequence-alignment program DIALIGN that has been developed for alignment of large genomic sequences. We compare our method to the alignment programs PipMaker, WABA and BLAST and we show that local similarities identified by these programs are highly correlated to protein-coding regions. In our test runs, PipMaker was the most sensitive method while DIALIGN was most specific.
  
  
  BACKGROUND
  The program is downloadable from the DIALIGN home page at http://bibiserv.techfak.uni-bielefeld.de/dialign/.
authors.affiliation: GSF Research Center, MIPS/Institute of Bioinformatics, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany. burkhard@TechFak.Uni-Bielefeld.DE
authors.forename: Burkhard
authors.initials: B
authors.lastname: Morgenstern
authors.forename: Oliver
authors.initials: O
authors.lastname: Rinner
authors.forename: Saïd
authors.initials: S
authors.lastname: Abdeddaïm
authors.forename: Dirk
authors.initials: D
authors.lastname: Haase
authors.forename: Klaus F X
authors.initials: KF
authors.lastname: Mayer
authors.forename: Andreas W M
authors.initials: AW
authors.lastname: Dress
authors.forename: Hans-Werner
authors.initials: HW
authors.lastname: Mewes
mesh_terms: D000818:Animals; D019295:Computational Biology; D019143:Evolution, Molecular; D005091:Exons; D023281:Genomics / Q000706:statistics & numerical data*; D006801:Humans; D051379:Mice; D016415:Sequence Alignment / Q000706:statistics & numerical data*; D012984:Software