Vmatch protocols

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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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Maintainer


  • person_outline Enno Ohlebusch <>

Publication for Vmatch

Vmatch in pipelines

 (16)
2017
PMCID: 5549432
PMID: 28789673
DOI: 10.1186/s13104-017-2671-0

[…] 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 […]

2017
PMCID: 5641073
PMID: 29069730
DOI: 10.18632/oncotarget.17776

[…] cell cultures with 137cs irradiator (mark 1 irradiator, jl shepherd & associates)., to search for direct repeat (dr) regions in mouse genome (mm9) and human genome (hg19) we used the program vmatch [] using the following parameters: minimal length of repeat region 480 bp, minimal gap between dr regions 500 bp, and maximal gap 50kb; minimal sequence identity between paired drs >97%, […]

2016
PMCID: 4726258
PMID: 26786968
DOI: 10.1038/srep19427

[…] proteomes at 35% and 75% cut-off were downloaded and hmm’s were generated from them using hmmer2.3.2. for clustering of the predicted elements each of the domains were grouped independently using vmatch and then ltr’s were grouped using the method used elsewhere. family classification of all the predicted elements was done as in wicker et al., using blastn and blastx searches against the trep […]

2016
PMCID: 4772642
PMID: 26925848
DOI: 10.1186/s12864-016-2440-9

[…] theoretically the overall synteny between the two genomes and can be recalculated in the upcoming releases of the assemblies, to be used in map validation. the list of mums was generated through vmatch (http://www.vmatch.de/). first mkvtree, part of vmatch, was used to generate an indexed database of x. tropicalis scaffolds sequences with options: −v dna -allout. then, we used vmatch command […]

2014
PMCID: 4251439
PMID: 25520706
DOI: 10.3389/fmicb.2014.00648

[…] suggests that those extremely common resistance genes could be present in multiple contexts and variants, and thereby cause velvet to perform sub-optimally. we therefore devised a scheme in which vmatch and trinity were used to iteratively construct contigs from reads associated with resistance genes. this way, we were able to assemble a 3579 bp contig containing sul2, a 2681 bp contig […]


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Vmatch in publications

 (81)
PMCID: 5954897
PMID: 29706510
DOI: 10.1016/j.cub.2018.03.041

[…] data for measuring trap stiffness. stall force data was digitized at 2 khz. thermal fluctuations were recorded at 40 khz. for measuring trap stiffness of phagosomes, the video-matching method (vmatch) was used. the linear range of both the qpd and optical trap had been measured separately. the chosen cut-off for measuring stalls is within the measured linear range of qpd. stall force […]

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

[…] the mitochondrial genome of s. lycopersici cidefi-216 has been deposited at ddbj/embl/genbank under the accession number kx453765., 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, […]

PMCID: 5549432
PMID: 28789673
DOI: 10.1186/s13104-017-2671-0

[…] 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 […]

PMCID: 5459504
PMID: 28542189
DOI: 10.1371/journal.pntd.0005559

[…] matching such a sequence. this is overcome (as done here) by pre-processing the utrs to remove low complexity stretches with dust [] and repeated sequence fragments with the rsat [] interface to the vmatch program (http://www.vmatch.de). finally, a significant scr signal can cause words that are very close to it to piggyback the signal and achieve elevated significance. this is then evident […]

PMCID: 5641073
PMID: 29069730
DOI: 10.18632/oncotarget.17776

[…] repeat sequences, we computationally identified paired dr motifs in the mouse genome with uniquely mapping locations and characteristics similar to dr-gfp8mu and dr-neomut8 reporters. using the vmatch program [], we identified 7,863 mouse dr pairs with the following parameters: 5′ and 3′ dr motifs each > 480 bp in the same orientation with 1–12 mismatched pairs (97%–99.9% identity) […]


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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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