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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

Documentation


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This tool is not available anymore.

Publication for HHsenser

HHsenser in publications

 (16)
PMCID: 5847487
PMID: 29092773
DOI: 10.1016/j.jsb.2017.10.010

[…] and error prone than the building of flip mcp., searching with default parameters for structures homologous to flip mcp with the hh-pred server (), no reasonable hits were found, whereas using hhsenser () one hit was found, comprising 38% sequence identity with a structural protein of the cellulophaga phage phi48:2, but no structure was available, making it impossible to start model […]

PMCID: 5372463
PMID: 28358387
DOI: 10.1038/srep45668

[…] 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., how to cite this article: akendengue, l. et al. bacterial kinesin light chain (bklc) links […]

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

[…] and cohesin smc1 and smc3, apparently indicating strict evolutionary conservation of arm length., to gain a more comprehensive view on the distribution of arm lengths in smc proteins, we used an hhsenser-based pipeline to aggregate large sets of diverged smc sequences () (). for each sequence, we identified the positions of head and hinge regions by sequence alignment and used the mean […]

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

[…] 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 […]

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

[…] self-associates via the 4-6 face, the protein does not form dimers either in solution or in cells., 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 […]


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

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