A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes.

ABSTRACT:

Background

Jumping alignments have recently been proposed as a strategy to search a given multiple sequence alignment A against a database. Instead of comparing a database sequence S to the multiple alignment or profile as a whole, S is compared and aligned to individual sequences from A. Within this alignment, S can jump between different sequences from A, so different parts of S can be aligned to different sequences from the input multiple alignment. This approach is particularly useful for dealing with recombination events.

Results

We developed a jumping profile Hidden Markov Model (jpHMM), a probabilistic generalization of the jumping-alignment approach. Given a partition of the aligned input sequence family into known sequence subtypes, our model can jump between states

SUBMITTER: Schultz AK 

PROVIDER: S-EPMC1525204 | biostudies-literature | 2006 May

REPOSITORIES: biostudies-literature