HHsenser: exhaustive transitive profile search using HMM–HMM comparison

By Johannes Söding, Michael Remmert, Andreas Biegert, Andrei N. Lupas. 2006

85 citations recorded by the source corpus.

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 . It has also been integrated into our structure and function prediction server HHpred () to improve predictions for near-singleton sequences.

Subfields: Molecular Biology

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In Molecular Biology

1. Cédric Notredame
2. Kazutaka Katoh
3. Robert C. Edgar
4. Hiroyuki Toh

Citations in the corpus

• The MPI Bioinformatics Toolkit for protein sequence analysis (2006, unknown): “In comparison (7).”
• The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis (2016, unknown): “Search CS-BLAST (6), HHblits (7), HHpred (5), HHsenser (45), HMMER3 (46), PatternSearch, ProtBLAST (9), ProtBLAST+ (15), PSI-BLAST (14), PSI-BLAST+ (15), SimShiftDB (47), PDBalert (37)”
• Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee (2012, background): “A natural consequence of these patterns conservation is the high sensitivity of profile-profile comparisons when doing remote homology search [9].”