HHrep specifications

Information


Unique identifier OMICS_10028
Name HHrep
Interface Web user interface
Restrictions to use None
Input data Protein sequence(s)
Computer skills Basic
Stability No
Maintained No

Maintainer


This tool is not available anymore.

Publication for HHrep

HHrep in publications

 (8)
PMCID: 5487470
PMID: 28702006
DOI: 10.3389/fmicb.2017.01145

[…] to see if expression of tb-mtra or the gain-of-function y102c tb-mtra in s. venezuelae would switch on chloramphenicol production. we also modeled sv-mtra onto the published tb-mtra structure using hhrep (; ) and made the equivalent y99c (predicted gain-of-function) change in sv-mtra (figure ). we made expression constructs for all three, driven by the s. venezuelae mtra promoter, […]

PMCID: 4827864
PMID: 27064789
DOI: 10.1371/journal.pone.0152733

[…] regions of an alignment. thus, all segments analyzed are derived from contiguous portions of proteins., the ancient rep (ar) and gsat programs [] were used to identify internal repeats, and the hhrep [] and hhrepid [] programs provided independent search approaches. the ar program compares potential transmembrane repeat sequences (e.g., transmembrane regions predicted by hmmtop) within […]

PMCID: 4590430
PMID: 26343760
DOI: 10.1016/j.jmb.2015.08.023

[…] 1, 4, 7, 10, 24 and 28) are present in apc5 tpr motifs . residues 1–208 n-terminal to the tpr domain do not conform to a tpr consensus sequence and no repeat motif was detected using tprpred and hhrep . based on secondary structure prediction (phyre2 ) and structure disorder programs (ond-crf ), residues 1–160 were predicted to be ordered and α-helical, with a disordered linker of ~ 30 […]

PMCID: 4345284
PMID: 25716199
DOI: 10.1098/rsob.150005

[…] in more than one third of the homologues; (v) strong indications of disruption of the sequence repeat pattern (not spanning multiples of seven positions) as revealed through alignment analyses with hhrep, hhrepid, and/or the coils/pcoils outputs at the bioinformatics toolkit site [] corroborated by other heuristics. ideally, we would like the fragment boundaries to coincide with locations […]

PMCID: 4096751
PMID: 24997568
DOI: 10.1186/1756-0500-7-435

[…] [] and coils (http://www.ch.embnet.org/software/coils_form.html) []. sequence repeats were predicted using rep (http://www.bork.embl.de/~andrade/papers/rep/search.html) [], hhrep (http://toolkit.tuebingen.mpg.de/hhrep) [] and repro (http://www.ibi.vu.nl/programs/reprowww/) []. fold recognition was performed using fugue (http://tardis.nibio.go.jp/fugue/) and hhpred […]


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HHrep institution(s)
Department for Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany; Gene Center Munich, University of Munich (LMU), Munich, Germany

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