Homology induction: the use of machine learning to improve sequence similarity searches.

ABSTRACT:

Background

The inference of homology between proteins is a key problem in molecular biology The current best approaches only identify approximately 50% of homologies (with a false positive rate set at 1/1000).

Results

We present Homology Induction (HI), a new approach to inferring homology. HI uses machine learning to bootstrap from standard sequence similarity search methods. First a standard method is run, then HI learns rules which are true for sequences of high similarity to the target (assumed homologues) and not true for general sequences, these rules are then used to discriminate sequences in the twilight zone. To learn the rules HI describes the sequences in a novel way based on a bioinformatic knowledge base, and the machine learning method of inductive logic progra

SUBMITTER: Karwath A 

PROVIDER: S-EPMC107726 | biostudies-literature | 2002 Apr

REPOSITORIES: biostudies-literature