Vmatch pipeline

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

Download


Versioning


Add your version

Maintainer


  • person_outline Enno Ohlebusch <>

Publication for Vmatch

Vmatch IN pipelines

 (12)
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 [68] 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 hmmer2.3.269. for clustering of the predicted elements each of the domains were grouped independently using vmatch70 and then ltr’s were grouped using the method used elsewhere68. family classification of all the predicted elements was done as in wicker et al.71, using blastn and blastx searches […]

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

[…] [32] was used to identify all possible open reading frames (orfs) for each gm and tc sequence. next, the longorf perl script was used to select the longest orf for each sequence. finally, the vmatch program (http://www.vmatch.de) was used to separately perform an “all-against-all” comparison for the gm datasets and each of the tc datasets. vmatch was used to translate the nucleotide […]

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

[…] all possible open reading frames (orfs) for each gm and tc sequence. next, the longorf perl script was used to select the longest orf for each sequence. finally, the vmatch program (http://www.vmatch.de) was used to separately perform an “all-against-all” comparison for the gm datasets and each of the tc datasets. vmatch was used to translate the nucleotide sequence of each gm and tc […]

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

[…] the longest orf for each sequence. finally, the vmatch program (http://www.vmatch.de) was used to separately perform an “all-against-all” comparison for the gm datasets and each of the tc datasets. vmatch was used to translate the nucleotide sequence of each gm and tc into six orfs and sequences were aligned using clustalw [40]. sequences with > 75 % similarity were considered “paralog […]

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.

Vmatch reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Vmatch