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HHsenser specifications

Information


Unique identifier OMICS_13611
Name HHsenser
Interface Web user interface
Restrictions to use None
Input data HHsenser takes a single query sequence or a multiple alignment as input.
Input format FASTA, CRUSTAL, Stockholm, A2M, A3M, EMBL, MEGA, GCG/MSF, PIR/NBRF, TREECON
Output data Returns two multiple alignments, a strict alignment and a permissive one.
Computer skills Basic
Stability No
Maintained No

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Publication for HHsenser

HHsenser citations

 (16)
library_books

Bacterial kinesin light chain (Bklc) links the Btub cytoskeleton to membranes

2017
Sci Rep
PMCID: 5372463
PMID: 28358387
DOI: 10.1038/srep45668

[…] to profile-based searches to search for eukaryotic homologues, using HHblits against the Uniprot database and HHsearch against the PDB. We also turned to transitive profile searches as implemented in HHsenser to explore distant homologues, as this method has proved to gather few false positive rates. […]

library_books

Tuned SMC Arms Drive Chromosomal Loading of Prokaryotic Condensin

2017
Mol Cell
PMCID: 5344682
PMID: 28238653
DOI: 10.1016/j.molcel.2017.01.026

[…] ucted with MSA-Probs (). Reference alignments for MukB, MksB and Rad50 were similarly constructed using sequences of the respective dimerization domains. Then, the alignments were used as queries for HHSenser searches (). The resulting sequence sets were filtered with PSI-BLAST for members containing significant homology to reference MSAs of N-terminal head (HeadN) and C-terminal head (HeadC) with […]

library_books

Sequence analysis reveals a conserved extension in the capping enzyme of the alphavirus supergroup, and a homologous domain in nodaviruses

2015
Biol Direct
PMCID: 4392871
PMID: 25886938
DOI: 10.1186/s13062-015-0050-0

[…] homology between families.Suggestion 1: It would be interesting to try to strengthen and describe the Alphavirus to Nodavirus link using the same or additional approaches. Besides HHpred and HHalign, HHsenser may be useful here as it allows intermediate HMM-HMM hits in the same framework to cover greater distances in sequence space (e.g. if starting alignment created by HHpred for a query has too […]

library_books

Vaccinia Virus Protein A49 Is an Unexpected Member of the B cell Lymphoma (Bcl) 2 Protein Family*

2015
PMCID: 4358236
PMID: 25605733
DOI: 10.1074/jbc.M114.624650

[…] Exhaustive searches of the NCBI nr (non-redundant) protein sequence database using PHMMER () and HHSENSER () yielded homologues of A49 only in orthopoxviruses and Yoka poxvirus. The genes encoding A49 homologues in ectromelia virus, taterapox virus, monkeypox virus, and camelpox virus are all sev […]

library_books

The Thalidomide Binding Domain of Cereblon Defines the CULT Domain Family and Is a New Member of the β Tent Fold

2015
PLoS Comput Biol
PMCID: 4287342
PMID: 25569776
DOI: 10.1371/journal.pcbi.1004023

[…] . Clustering was done in default settings (attract = 10, repulse = 5, exponents = 1), with other settings as given in the figure legends.Searches for more distant homologs were made with HHpred and HHsenser on the databases pdb70 (sequences of protein databank structures, as available in April 2014, clustered at 70% sequence identity), CDD (conserved domain database from NCBI, as of February 20 […]

library_books

Diversity and Variability of NOD Like Receptors in Fungi

2014
Genome Biol Evol
PMCID: 4986451
PMID: 25398782
DOI: 10.1093/gbe/evu251

[…] ents in terms of the normalized Median Distance (norMD, []) were used for the HMM training with default parameters (). A single representative sequence for each nonprionic domain was submitted to the HHsenser web tool (PSI-BLAST parameters: E value cut-off of 10−3, coverage of hits at least 50% []) to build a data set including at least 500 sequences in the “permissive” alignment. “Strict” alignme […]


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HHsenser institution(s)
Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, Tubingen, Germany

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