AnABlast: a new in silico strategy for the genome-wide search of novel genes and fossil regions.
Genome annotation, assisted by computer programs, is one of the great advances in modern biology. Nevertheless, the in silico identification of small and complex coding sequences is still challenging. We observed that amino acid sequences inferred from coding-but rarely from non-coding-DNA sequences accumulated alignments in low-stringency BLAST searches, suggesting that this alignments accumulation could be used to highlight coding regions in sequenced DNA. To investigate this possibility, we developed a computer program (AnABlast) that generates profiles of accumulated alignments in query amino acid sequences using a low-stringency BLAST strategy. To validate this approach, all six-frame translations of DNA sequences between every two annotated exons of the fission yeast genome were analysed with AnABlast. AnABlast-generated profiles identified three new copies of known genes, and four new genes supported by experimental evidence. New pseudogenes, ancestral carboxyl- and amino-terminal subtractions, complex gene rearrangements, and ancient fragments of mitDNA and of bacterial origin, were also inferred. Thus, this novel in silico approach provides a powerful tool to uncover new genes, as well as fossil-coding sequences, thus providing insight into the evolutionary history of annotated genomes.
Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide de Sevilla/CSIC, Sevilla, Spain jjimmar@upo.es.
Juan
J
Jimenez
Department of Biochemistry, University of Cambridge, Cambridge, UK.
Caia D S
CD
Duncan
Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide de Sevilla/CSIC, Sevilla, Spain.
María
M
Gallardo
Department of Biochemistry, University of Cambridge, Cambridge, UK.
Juan
J
Mata
Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide de Sevilla/CSIC, Sevilla, Spain.
Antonio J
AJ
Perez-Pulido
D003198:Computer Simulation; D019143:Evolution, Molecular; D056726:Genetic Association Studies / Q000379:methods*; D016681:Genome, Fungal; D007438:Introns; D011544:Pseudogenes; D012568:Schizosaccharomyces / Q000235:genetics*; D016415:Sequence Alignment
Schizosaccharomyces pombe; fossil DNA sequences; genome evolution; in silico annotation tool; new genes