A kingdom-specific protein domain HMM library for improved annotation of fungal genomes.

ABSTRACT:

Background

Pfam is a general-purpose database of protein domain alignments and profile Hidden Markov Models (HMMs), which is very popular for the annotation of sequence data produced by genome sequencing projects. Pfam provides models that are often very general in terms of the taxa that they cover and it has previously been suggested that such general models may lack some of the specificity or selectivity that would be provided by kingdom-specific models.

Results

Here we present a general approach to create domain libraries of HMMs for sub-taxa of a kingdom. Taking fungal species as an example, we construct a domain library of HMMs (called Fungal Pfam or FPfam) using sequences from 30 genomes, consisting of 24 species from the ascomycetes group and two basidiomycetes, Ustil

SUBMITTER: Alam I 

PROVIDER: S-EPMC1854895 | biostudies-literature | 2007 Apr

REPOSITORIES: biostudies-literature