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HHrep specifications

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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

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Publication for HHrep

HHrep citations

 (8)
library_books

The Conserved Actinobacterial Two Component System MtrAB Coordinates Chloramphenicol Production with Sporulation in Streptomyces venezuelae NRRL B 65442

2017
Front Microbiol
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, […]

library_books

Properties and Phylogeny of 76 Families of Bacterial and Eukaryotic Organellar Outer Membrane Pore Forming Proteins

2016
PLoS One
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 […]

library_books

Atomic Resolution Structures of the APC/C Subunits Apc4 and the Apc5 N Terminal Domain

2015
J Mol Biol
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 […]

library_books

Three dimensional topology of the SMC2/SMC4 subcomplex from chicken condensin I revealed by cross linking and molecular modelling

2015
Open Biol
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 […]

library_books

Brefeldin A inhibited guanine nucleotide exchange protein 3 (BIG3) is predicted to interact with its partner through an ARM type α helical structure

2014
BMC Res Notes
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 […]

library_books

Ab initio detection of fuzzy amino acid tandem repeats in protein sequences

2012
BMC Bioinformatics
PMCID: 3402919
PMID: 22536906
DOI: 10.1186/1471-2105-13-S3-S8

[…] more recently newman and cooper proposed xstream [], which uses a seed expansion approach, while jorda and kajava proposed t-reks [], which uses a clustering approach based on k-means. the systems hhrep [] and hhrepid [] are instead based on building and matching hidden markov models for the repeating substrings to be sought (not necessarily tandem). some approaches based on neuronal networks […]


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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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