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Bioinformatics Vol. 17 no. 1 2001
Pages 13-15
© 2001 Oxford University Press

Original Paper

Pro-Frame: similarity-based gene recognition in eukaryotic DNA sequences with errors

Andrey A. Mironov , Pavel S. Novichkov and Mikhail S. Gelfand

State Scientific Center for Biotechnology NIIGenetika, Moscow, 113545, Russia

Received on September 22, 1999 ; revised on June 5, 2000 ; accepted on July 27, 2000

Summary: Performance of existing algorithms for similarity-based gene recognition in eukaryotes drops when the genomic DNA has been sequenced with errors. A modification of the spliced alignment algorithm allows for gene recognition in sequences with errors, in particular frameshifts. It tolerates up to 5% of sequencing errors without considerable drop of prediction reliability when a sufficiently close homologous protein is available (normalized evolutionary distance similarity score 50% or higher).

Availability: The program is free for academic users and available upon request at http://www.anchorgen.com

Contact: mgelfand{at}anchorgen.com


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