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HHsenser: Exhaustive transitive profile search using HMM-HMM comparison

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Söding,  J       
Department Protein Evolution, Max Planck Institute for Developmental Biology, Max Planck Society;

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Remmert,  M
Department Protein Evolution, Max Planck Institute for Developmental Biology, Max Planck Society;

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Biegert,  A
Department Protein Evolution, Max Planck Institute for Developmental Biology, Max Planck Society;

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Lupas,  AN       
Department Protein Evolution, Max Planck Institute for Developmental Biology, Max Planck Society;

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Citation

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


Cite as: https://hdl.handle.net/21.11116/0000-000B-4361-C
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.