title: A comparative analysis of computational motif-detection methods.
abstract: The detection of motifs within and among families of protein sequences can provide useful information regarding the function, structure and evolution of a protein. With the increasing number of computer programs available for motif detection, a comparative evaluation of the programs from a biological perspective is warranted. This study uses a set of 20 reverse transcriptase (RT) protein sequences to test and compare the ability of 7 different computational methods to locate the ordered-series-of-motifs that are well characterized in the RT sequences. The results provide insight to biologists as to the usage, value, and reliability of the numerous methods available.
authors.affiliation: Department of Biological Sciences, University of Nevada, Las Vegas 89154-4004, USA.
authors.forename: J
authors.initials: J
authors.lastname: Hudak
authors.forename: M A
authors.initials: MA
authors.lastname: Mcclure
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D016384:Consensus Sequence; D016208:Databases, Factual; D016681:Genome, Fungal; D008969:Molecular Sequence Data; D012194:RNA-Directed DNA Polymerase / Q000737:chemistry* / Q000235:genetics; D016914:Ribonuclease H / Q000737:chemistry* / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000201:enzymology / Q000235:genetics*; D016415:Sequence Alignment; D012984:Software
chemical_list: D012194:RNA-Directed DNA Polymerase; D016914:Ribonuclease H