QuasiMotiFinder: protein annotation by searching for evolutionarily conserved motif-like patterns.

ABSTRACT: Sequence signature databases such as PROSITE, which include amino acid segments that are indicative of a protein's function, are useful for protein annotation. Lamentably, the annotation is not always accurate. A signature may be falsely detected in a protein that does not carry out the associated function (false positive prediction, FP) or may be overlooked in a protein that does carry out the function (false negative prediction, FN). A new approach has emerged in which a signature is replaced with a sequence profile, calculated based on multiple sequence alignment (MSA) of homologous proteins that share the same function. This approach, which is superior to the simple pattern search, essentially searches with the sequence of the query protein against an MSA library. We suggest here an al

SUBMITTER: Gutman R 

PROVIDER: S-EPMC1160256 | biostudies-literature | 2005 Jul

REPOSITORIES: biostudies-literature