A model-based information sharing protocol for profile Hidden Markov Models used for HIV-1 recombination detection.

ABSTRACT:

Background

In many applications, a family of nucleotide or protein sequences classified into several subfamilies has to be modeled. Profile Hidden Markov Models (pHMMs) are widely used for this task, modeling each subfamily separately by one pHMM. However, a major drawback of this approach is the difficulty of dealing with subfamilies composed of very few sequences. One of the most crucial bioinformatical tasks affected by the problem of small-size subfamilies is the subtyping of human immunodeficiency virus type 1 (HIV-1) sequences, i.e., HIV-1 subtypes for which only a small number of sequences is known.

Results

To deal with small samples for particular subfamilies of HIV-1, we introduce a novel model-based information sharing protocol. It estimates the emission probabilit

SUBMITTER: Bulla I 

PROVIDER: S-EPMC4230192 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature