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HHrepID specifications

Information


Unique identifier OMICS_10037
Name HHrepID
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Protein sequence(s)
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Johannes Soeding <>

Information


Unique identifier OMICS_10037
Name HHrepID
Interface Web user interface
Restrictions to use None
Input data Protein sequence(s)
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Johannes Soeding <>

Publication for HHrepID

HHrepID in pipeline

2010
PMCID: 2954813
PMID: 20976240
DOI: 10.1371/journal.pone.0013402

[…] and b. burgdorferi was obtained in the following way: we first aligned full-length human pur-α with d. melanogaster pur-α using clustalw . then we submitted the pair-wise alignment to the hhrepid server to obtain an accurate alignment of the three pur repeats, from which the multiple alignment of the six repeats from human and d. melanogaster pur-α was manually reconstructed. to add […]

HHrepID in publications

 (25)
PMCID: 5892909
PMID: 29634783
DOI: 10.1371/journal.pone.0195656

[…] localization and the presence of chloroplast transit peptides were checked with targetp [] and chlorop [], respectively. internal sequence repeats were identified with the de novo prediction server hhrepid []., r-pe from g. ch was purified as described previously [] and the separation of subunits was performed as reported by apt et al. (1993)[] and sepúlveda ugarte et al. (2011)[], […]

PMCID: 5868767
PMID: 29579047
DOI: 10.1371/journal.pone.0192851

[…] to identify repeat sequences in members of the anoctamin superfamily. however, it was not possible to find significant evidence suggestive of the occurrence of internal sequence repeats using the hhrepid [] and ancientrep [] programs. similarly, examination of the 3-d structure of the fungal homologue, nhtnem16, failed to reveal the presence of reliable repeat structures. however, […]

PMCID: 5461629
PMID: 28587627
DOI: 10.1186/s12870-017-1042-2

[…] here. mammalian perilipins attach by means of amphipathic helices, which are formed by tandem repeats in the amino acid sequence []. a search for such repeats in the lilbps described here using hhrepid [, ] yielded no results. this is also the case for a range of other proteins that are known to associate with lbs including algal mldps [, , ]. these proteins possibly attach to the lb […]

PMCID: 5120217
PMID: 27857066
DOI: 10.1038/ncomms13570

[…] for major expansions of the proteome at evolutionary transitions, such as the origin of eukaryotes. however, it should be noted that for highly diverged repeats, such as those identified by hhrepid, where estimates of dn/ds are often unattainable, the net effect of selection might be closer to neutrality (). furthermore, the biphasic evolutionary model formulated here represents […]

PMCID: 5100051
PMID: 27671125
DOI: 10.1093/molbev/msw194

[…] ancestral gene and multiple sequence alignments (msas) are provided for each family. we scanned 15,322 treefam families for the presence of repeats with a minimum unit length of 12 amino acids using hhrepid (). whereas most approaches for de novo identification of repeats rely on comparing a protein sequence to itself, hhrepid further utilizes evolutionary information by aligning homologous […]

HHrepID 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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