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Repseek specifications

Information


Unique identifier OMICS_03542
Name Repseek
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Repseek

Repseek citations

 (3)
library_books

The Complete Genome Sequence of the Fish Pathogen Tenacibaculum maritimum Provides Insights into Virulence Mechanisms

2017
Front Microbiol
PMCID: 5561996
PMID: 28861057
DOI: 10.3389/fmicb.2017.01542

[…] performed using the web interface MicroScope () which allows graphic visualization enhanced by a synchronized representation of synteny groups. Predictions of repeated sequences were performed using Repseek () and those of genomic islands (GIs) using SIGI-HMM () and Alien hunter (). The dbCAN database was used to identify carbohydrate active enzymes (CAZymes) (). The genomic sequence reported in […]

call_split

Sister Dehalobacter Genomes Reveal Specialization in Organohalide Respiration and Recent Strain Differentiation Likely Driven by Chlorinated Substrates

2016
Front Microbiol
PMCID: 4751268
PMID: 26903979
DOI: 10.3389/fmicb.2016.00100
call_split See protocol

[…] DNA sequences, such as single genes, were performed by MUSCLE (Edgar, ) within Geneious pro. Genome circular maps were created with BRIG (Alikhan et al., ). DNA sequence repeats were identified with Repseek (Achaz et al., ) and inverted repeats were identified with Inverted Repeat Finder (Warburton et al., ). Orthologs between Dehalobacter genomes were identified with reciprocal BLASTP with an e- […]

library_books

A Tribute to Disorder in the Genome of the Bloom Forming Freshwater Cyanobacterium Microcystis aeruginosa

2013
PLoS One
PMCID: 3741299
PMID: 23950996
DOI: 10.1371/journal.pone.0070747

[…] as gene pairs satisfying an alignment threshold of at least 50% amino acid sequence identity over at least 50% of the length of the smallest protein.The proportion of repeats was estimated using the Repseek algorithm. This algorithm is a fast two-step method (seed detection followed by their extensions), which allows finding large degenerate repeats within or between large DNA sequences .The synt […]

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Repseek institution(s)
Atelier de Bioinformatique, Université Pierre et Marie Curie-Paris, Paris, France

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