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Repseek specifications


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


No version available

Publication for Repseek

Repseek citations


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

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 […]


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

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- […]


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

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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