title: FASSM: enhanced function association in whole genome analysis using sequence and structural motifs.
abstract: We present an algorithm to detect remote homology, which arises through circular permutation and discontinuous domains. It is also helpful in detecting small domain proteins that are characterized by few conserved residues. The input to the algorithm is a set of multiply aligned protein sequence profiles. This method, coded as FASSM, examines the sequence conservation and positions of protein family signatures or motifs for the annotation of protein sequences and to facilitate the analysis of their domains. The overall coverage of FASSM is 93% in comparison to other validation tools like HMM and IMPALA. The method is especially useful for difficult relationships such as discontinuous domains during whole-genome surveys and is demonstrated to perform accurate family associations at sequence identities as low as 15%.
authors.affiliation: National Centre for Biological Sciences, UAS-GKVK campus, Bellary Road, Bangalore 560 065, India.
authors.forename: Kumar
authors.initials: K
authors.lastname: Gaurav
authors.forename: Nitin
authors.initials: N
authors.lastname: Gupta
authors.forename: Ramanathan
authors.initials: R
authors.lastname: Sowdhamini
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D017124:Conserved Sequence; D030562:Databases, Protein; D048168:Escherichia coli K12 / Q000201:enzymology / Q000235:genetics; D023281:Genomics / Q000706:statistics & numerical data*; D008780:Methyltransferases / Q000737:chemistry / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016571:Neural Networks, Computer; D010802:Phylogeny; D011506:Proteins / Q000737:chemistry* / Q000235:genetics*; D040901:Proteomics / Q000706:statistics & numerical data; D016415:Sequence Alignment / Q000706:statistics & numerical data
chemical_list: D011506:Proteins; D008780:Methyltransferases; C434266:S-adenosyl-L-methionine-dependent N-methyltransferase