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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 in publications

 (8)
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 […]

PMCID: 5345009
PMID: 28281695
DOI: 10.1038/srep44331

[…] bacterial genome sequences were retrieved from genbank and analysed for the presence of large inverted repeats comparable to those found in the l. delbrueckii ssp. bulgaricus atcc11842 genome using repseek with the following parameters: -l 1000 (repetition >1000 bp), -c (circular chromosome), -i (inverted repeats). the results were filtered to keep only inverted repeats where the size […]

PMCID: 5378121
PMID: 28188144
DOI: 10.1534/genetics.116.196154

[…] mislead the bacterial dsb recombinational-repair system into creating genomic rearrangements by using ectopic repeats for the reattachment of dna strands (). repetitive sequences were detected using repseek (). exact repeats can be reported by repseek based on (i) preset minimal length of the repeat, or (ii) preset maximal p-value of the repeat length. repseek assigns a p-value to exact repeats […]

PMCID: 4751268
PMID: 26903979
DOI: 10.3389/fmicb.2016.00100

[…] 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 […]

PMCID: 4201751
PMID: 25011705
DOI: 10.1007/s00294-014-0436-z

[…] the probability of finding such an orf by chance was equal to finding a 420 bp orf in h. irregulare, given the base composition of the species. repeats were detected in the species with the program repseek (achaz et al. ) using a cutoff p value of 0.01. some additional annotation of the intronic orfs was done in cryptococcus neoformans, phakopsora meibomiae, p. pachyrhizi, trametes cingulata, […]


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

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