Vmatch statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Vmatch
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Tool usage distribution map

This map represents all the scientific publications referring to Vmatch per scientific context
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Associated diseases

This word cloud represents Vmatch usage per disease context
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Popular tool citations

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Protocols

Vmatch specifications

Information


Unique identifier OMICS_19963
Name Vmatch
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format FASTA, GENBANK, EMBL, SWISSPROT
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 2.3.0
Stability Stable
Maintained Yes

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Versioning


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Maintainer


  • person_outline Enno Ohlebusch

Publication for Vmatch

Vmatch citations

 (51)
library_books

The mitochondrial genome of the plant pathogenic fungus Stemphylium lycopersici uncovers a dynamic structure due to repetitive and mobile elements

2017
PLoS One
PMCID: 5626475
PMID: 28972995
DOI: 10.1371/journal.pone.0185545

[…] Repetitive sequences were identified using the Vmatch software (http://www.vmatch.de/). Both direct and inverted repeats (palindromes) were computed by extending a seed of 30 nucleotides in length in both directions allowing for matches, mismatche […]

library_books

Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep

2017
BMC Res Notes
PMCID: 5549432
PMID: 28789673
DOI: 10.1186/s13104-017-2671-0

[…] iptome datasets were constructed as previously described []. Assemblies were combined, and duplicated contigs, or smaller contigs covered by larger ones, were removed using the clustering function in Vmatch (http://www.vmatch.de). The resulting contigs were submitted to IMG/Mer [] for gene-calling and automatic annotation. All assembled genes with hits to the relevant KEGG genes were extracted and […]

library_books

Many si/shRNAs can kill cancer cells by targeting multiple survival genes through an off target mechanism

2017
eLife
PMCID: 5655136
PMID: 29063830
DOI: 10.7554/eLife.29702.033

[…] Ensembl, version 76. As required by Sylamer, they were cleaned of low-complexity sequences and repetitive fragments using respectively Dust () with default parameters and the RSAT interface () to the Vmatch program, also run with default parameters. Sylamer (version 12–342) was run with the Markov correction parameter set to 4. […]

library_books

Transcriptome sequencing reveals high isoform diversity in the ant Formica exsecta

2017
PeerJ
PMCID: 5701548
PMID: 29177112
DOI: 10.7717/peerj.3998

[…] es of libraries, platforms, and read lengths. Initial-TA contigs from Trinity were chosen to build a combined assembly (Meta-TA) from different k-mer runs (, ) by scaffolding overlapping contigs with Vmatch software (). This procedure results in a non-redundant set of contig sequences originating from the initial k-mer specific Trinity assemblies. The merged Meta-TA assembly produced a total of 23 […]

library_books

A Comprehensive Curation Shows the Dynamic Evolutionary Patterns of Prokaryotic CRISPRs

2016
Biomed Res Int
PMCID: 4852346
PMID: 27195295
DOI: 10.1155/2016/7237053

[…] s nature of local scanning, CRT runs for linear time and within linear memory space. Its default setting for DR lengths is between 21 and 37 bps. The latest tool CRISPRFinder [] uses an existing tool Vmatch to find the DR array in a given genome and will discard the tandem repeats as false positives. CRISPRFinder has a slightly longer assumption for DRs between 20 and 47 bps. A comprehensive datab […]

library_books

Paralog analyses reveal gene duplication events and genes under positive selection in Ixodes scapularis and other ixodid ticks

2016
BMC Genomics
PMCID: 4793754
PMID: 26984180
DOI: 10.1186/s12864-015-2350-2

[…] I. scapularis GMs (293 clusters of size two with Vmatch and 160 paralog pairs with PAML analysis; low stringency level) than in the sampled transcriptome (TC dataset) (1443 clusters of size two with Vmatch and 1128 paralog pairs with PAML analysis; low stringency level) (Tables ; Additional file : Table S1). Paralog pairs represent ~1-2 % of the gene complement, and this is lower than percentages […]


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Vmatch institution(s)
Faculty of Computer Science, University of Ulm, Ulm, Germany; Center for Bioinformatics, University of Hamburg, Hamburg, Germany
Vmatch funding source(s)
Supported by DFG-grant Oh 54/4-1, and the DFG-grant Ku 1257/1-3.

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