Nucleic Acids Research, 1994, Vol. 22, No. 22 4768-4778
© 1994
COMPUTATIONAL BIOLOGY |
A hidden Markov model that finds genes in E.coli DNA
Nordita, Blegdamsvej 17, DK-2100 Copenhagen, Denmark 1Sinsheimer Laboratories, University of California Santa Cruz, CA 95064 2Computer and Information Sciences, Univesity of California Santa Cruz, CA 95064, USA
*To whom correpsondence should be addressed
Received June 21, 1994. Revised September 28, 1994. Accepted September 28, 1994.
A hidden Markov model (HMM) has been developed to find protein coding genes in E.coli DNA using E.coli genome DNA sequence from the EcoSeq6 database maintained by Kenn Rudd. This HMM includes states that model the codons and their frequencies in E.coli genes, as well as the patterns found in the intergenic region, including repetitive extragenic palindromic sequences and the Shine – Delgarno motif. To account for potential sequencing errors and or frameshifts in raw genomic DNA sequence, it allows for the (very unlikely) possiblity of insertions and deletions of individual nucleotides within a codon. The parameters of the HMM are estimated using approximately one million nucleotides of annotated DNA in EcoSeq6 and the model tested on a disjoint set of contigs containing about 325,000 nucleotides. The HMM finds the exact locations of about 80% of the known E.coli genes, and approximate locations for about 10%. It also finds several potentially new genes, and locates several places were insertion or deletion errors/and or frameshifts may be present in the contigs.
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