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Journal Article

HHsenser: Exhaustive transitive profile search using HMM-HMM comparison.


Söding,  J.
Research Group of Computational Biology, MPI for Biophysical Chemistry, Max Planck Society;

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Söding, J., Remmert, M., Biegert, A., & Lupas, A. N. (2006). HHsenser: Exhaustive transitive profile search using HMM-HMM comparison. Nucleic Acids Research (London), 34, W374-W378. doi:10.1093/nar/gkl195.

Cite as: http://hdl.handle.net/11858/00-001M-0000-0017-E9C2-0
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.