title: HHsenser: exhaustive transitive profile search using HMM-HMM comparison.
abstract: HHsenser is the first server to offer exhaustive intermediate profile searches, which it combines with pairwise comparison of hidden Markov models. Starting from a single protein sequence or a multiple alignment, it can iteratively explore whole superfamilies, producing few or no false positives. The output is a multiple alignment of all detected homologs. HHsenser's sensitivity should make it a useful tool for evolutionary studies. It may also aid applications that rely on diverse multiple sequence alignments as input, such as homology-based structure and function prediction, or the determination of functional residues by conservation scoring and functional subtyping.HHsenser can be accessed at http://hhsenser.tuebingen.mpg.de/. It has also been integrated into our structure and function prediction server HHpred (http://hhpred.tuebingen.mpg.de/) to improve predictions for near-singleton sequences.
authors.affiliation: Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany. johannes.soeding@tuebingen.mpg.de
authors.forename: Johannes
authors.initials: J
authors.lastname: Söding
authors.forename: Michael
authors.initials: M
authors.lastname: Remmert
authors.forename: Andreas
authors.initials: A
authors.lastname: Biegert
authors.forename: Andrei N
authors.initials: AN
authors.lastname: Lupas
mesh_terms: D020407:Internet; D008390:Markov Chains; D016415:Sequence Alignment / Q000379:methods*; D017421:Sequence Analysis; D020539:Sequence Analysis, Protein; D017386:Sequence Homology, Amino Acid; D012984:Software; D014584:User-Computer Interface