SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model.

ABSTRACT: Comparative-based gene recognition is driven by the principle that conserved regions between related organisms are more likely than divergent regions to be coding. We describe a probabilistic framework for gene structure and alignment that can be used to simultaneously find both the gene structure and alignment of two syntenic genomic regions. A key feature of the method is the ability to enhance gene predictions by finding the best alignment between two syntenic sequences, while at the same time finding biologically meaningful alignments that preserve the correspondence between coding exons. Our probabilistic framework is the generalized pair hidden Markov model, a hybrid of (1). generalized hidden Markov models, which have been used previously for gene finding, and (2). pair hidden Marko

SUBMITTER: Alexandersson M 

PROVIDER: S-EPMC430255 | biostudies-literature | 2003 Mar

REPOSITORIES: biostudies-literature