Internal Repeats Finder statistics

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Internal Repeats Finder specifications

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Unique identifier OMICS_10031
Name Internal Repeats Finder
Interface Web user interface
Restrictions to use None
Input data Protein sequence
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 3.0
Computer skills Basic
Stability No
Source code URL http://www.lbgi.fr/VaRank/downloads.html
Maintained No

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Publications for Internal Repeats Finder

Internal Repeats Finder citations

 (3)
library_books

Genomics of Clostridium taeniosporum, an organism which forms endospores with ribbon like appendages

2018
PLoS One
PMCID: 5749712
PMID: 29293521
DOI: 10.1371/journal.pone.0189673

[…] pipeline.The replication origin, oriC, was found by Ori-Finder []. Similarity of (deduced) protein sequences was monitored with Lalign version 36.3.5e [], internal repeat sequences were detected with Internal Repeats Finder [], DUF11 was located with MyHits [] and putative promoters located by Pattern Locator []. Prophage sequences were identified and annotated by PHAST (http://phast.wishartlab.co […]

library_books

KIAA0556 is a novel ciliary basal body component mutated in Joubert syndrome

2015
Genome Biol
PMCID: 4699358
PMID: 26714646
DOI: 10.1186/s13059-015-0858-z

[…] xiterate 1000) and MUSCLE [], and manually curated in JalView []. JalView was used for sequence visualisation. The internal repeats of human KIAA0556 and its orthologues were detected using RADAR [], Internal Repeats Finder [], Pfam [], and SMART []. HHPred [] was used to detect and evaluate the remote homology between the KIAA0556 repeats (including the permutated versions) and IFT25, taking into […]

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

[…] [] T-REKS and other programs are compared by analyzing an old version of the Swiss-Prot database (Release of January 2009), which contained 356, 232 sequences. Among the four evaluated tools (T-REKS, Internal Repeats Finder [], XSTREAM [], and TRED []), T-REKS is the one that provided the best results by identifying 33, 780 sequences as containing TRs. The definition of TR used by T-REKS is the fo […]


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Internal Repeats Finder institution(s)
Molecular Biology Institute and UCLA-DOE Laboratory of Structural Biology and Molecular Medicine, University of California, Los Angeles, Los Angeles, CA, USA
Internal Repeats Finder funding source(s)
Supported by grants and fellowships from Agence de Biom├ędecine, Fondation Jerome Lejeune, APLM, CREGEMES, INSERM and ANR-11-BSV1-026-01.

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