title: Gene recognition in eukaryotic DNA by comparison of genomic sequences.
abstract: BACKGROUND
  Sequencing of complete eukaryotic genomes and large syntenic fragments of genomes makes it possible to apply genomic comparison for gene recognition.
  
  
  RESULTS
  This paper describes a spliced alignment algorithm that aligns candidate exon chains of two homologous genomic sequence fragments from different species. The algorithm is implemented in Pro-Gen software. Unlike other algorithms, Pro-Gen does not assume conservation of the exon-intron structure. Amino acid sequences obtained by the formal translation of candidate exons are aligned instead of nucleotide sequences, which allows for distant comparisons. The algorithm was tested on a sample of human-mammal (mouse), human-vertebrate (Xenopus ) and human-invertebrate (Drosophila ) gene pairs. Surprisingly, the best results, 97-98% correlation between the actual and predicted genes, were obtained for more distant comparisons, whereas the correlation on the human-mouse sample was only 93%. The latter value increases to 95% if conservation of the exon-intron structure is assumed. This is caused by a large amount of sequence conservation in non-coding regions of the human and mouse genes probably due to regulatory elements.
  
  
  BACKGROUND
  Pro-Gen v. 3.0 is available to academic researchers free of charge at http://www.anchorgen.com/pro_gen/pro_gen.html.
authors.affiliation: State Scientific Center GosNIIGenetika, 1 Dorozhny pr. 1, Moscow 113545, Russia.
authors.forename: P S
authors.initials: PS
authors.lastname: Novichkov
authors.forename: M S
authors.initials: MS
authors.lastname: Gelfand
authors.forename: A A
authors.initials: AA
authors.lastname: Mironov
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology; D004247:DNA / Q000235:genetics*; D004330:Drosophila / Q000235:genetics; D005057:Eukaryotic Cells; D005091:Exons; D016678:Genome; D006801:Humans; D051379:Mice; D016415:Sequence Alignment / Q000706:statistics & numerical data; D012984:Software; D014981:Xenopus / Q000235:genetics
chemical_list: D004247:DNA