P-Match protocols

View P-Match computational protocol

P-Match statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Motif scanning chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

P-Match specifications

Information


Unique identifier OMICS_18433
Name P-Match
Interface Web user interface
Restrictions to use None
Input data A library of weight matrices, a profile file containing a set of matrix accession numbers, a DNA sequence file.
Input format TRANSFAC, FASTA EMBL
Programming languages C++, Perl
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Kel AE <>

Additional information


A registration is needed to access to tool.

Information


Unique identifier OMICS_18433
Name P-Match
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A library of weight matrices, a profile file containing a set of matrix accession numbers, a DNA sequence file.
Input format TRANSFAC, FASTA EMBL
Operating system Unix/Linux, Windows
Programming languages C++, Perl
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


Add your version

Maintainer


  • person_outline Kel AE <>

Additional information


A registration is needed to access to tool.

Publication for P-Match

P-Match in pipelines

 (3)
2012
PMCID: 3264657
PMID: 22292071
DOI: 10.1371/journal.pone.0030895

[…] (tarsius syrichta) sequences were identified from the whole-genome shotgun sequence database in ncbi using blastn . sequence alignment was performed using multi-lagan and visualized in bioedit . p-match was used for identification and scoring of yy1 dna response elements. matching was performed to predefined vertebrate matrices in a liver specific profile., the proximal 370 bp of the cyp3a5 […]

2011
PMCID: 3325368
PMID: 21383772
DOI: 10.1038/tpj.2011.8

[…] a priori probabilities of being functional, such as proximal to the transcription start site, in the 3′-utr, or in the first intron, iii) predicted to alter binding of transcription factors by the p-match (http://www.gene-regulation.com), tf-search (http://www.cbrc.jp/research/db/tfsearch.html) or the deltamatch software, or iv) located in a region conserved between humans and other placental […]

2009
PMCID: 3087513
PMID: 19943979
DOI: 10.1186/1471-2156-10-76

[…] table . after incubation at 37°c the resulting fragments were separated on a 2% agarose gel., *polymorphic nucleotide marked in bold, transcription factor binding sites were predicted by cister [], p-match [] and matinspector []. prediction of mrna secondary structure was carried out using the mfold web server []., haplotypes were inferred using phase software version 2.1.1 [,] with default […]


To access a full list of citations, you will need to upgrade to our premium service.

P-Match in publications

 (50)
PMCID: 5626709
PMID: 28974731
DOI: 10.1038/s41598-017-12955-7

[…] roscoff, france) (http://rsat.eu), nsite (version 5.2013, softberry, inc., mount kisco, ny, usa) (http://www.softberry.com/berry.phtml?topic = nsite&group = help&subgroup = promoter) and p-match-1.0 (helmholtz centre for infection research; transfac/biobase gmbh, braunschweig, germany) (http://gene-regulation.com/pub/programs.html) software tools predicted a large number […]

PMCID: 5593964
PMID: 28894234
DOI: 10.1038/s41598-017-11627-w

[…] represent the neighbor cpg sites. in addition, ucsc genome browser website showed that the fragment was overlapped with several transcription factors binding sites, such as ctcf and znf143. we used p-match method to predict tfbs in the selected fragment, there were nkx2-5, c-rel, nf-kappab(p65), nf-kappab in this fragment. further study should be performed to explore the regulatory roles of cpg […]

PMCID: 5579262
PMID: 28860510
DOI: 10.1038/s41598-017-10465-0

[…] (computational biology research center, national institute of advanced industrial science and technology, tsukuba, japan), matinspector (genomatrix software, munchen, germany), tfblast, tfsitescan, p-match, signal scan and the jaspar database. the criteria for the selection of potential gre sites consisted of sequence identification by at least 3 software algorithms with a score greater […]

PMCID: 5663546
PMID: 29137374
DOI: 10.18632/oncotarget.19016

[…] by means of the following online tools using different algorithms for the prediction of the presence of transcription factor binding sites: matinspector (genomatix.de) [], match, patch, p-match [, ], and alibaba2 (gene-regulation.com) []. for the analysis of evolutionarily conserved putative hres, the rvista 2.0 tool (rvista.dcode.org) was employed as described previously []. […]

PMCID: 5450854
PMID: 28537227
DOI: 10.12659/MSM.902109

[…] value of p<0.05 was considered as statistically significant. all analyses were carried out by using spss (version 16.0; spss inc., chicago, illinois, usa) and adjusted for age, sex, and bmi., p-match is a kind of functional prediction tool (http://www.gene-regulation.com/cgi-bin/pub/programs/pmatch/bin/pmatch.cgi), which is used to predict the effects of polymorphisms on the sequence […]


To access a full list of publications, you will need to upgrade to our premium service.

P-Match institution(s)
BIOBASE GmbH, Wolfenbuttel, Germany
P-Match funding source(s)
Supported by a grant of the European Commission (Projects: Intergenomics, COMBIO, INTAS:N.03-51- 5218, TRANSISTOR), and by grant BioProfile Braunschweig/ Gottingen/Hannover (0 313 092).

P-Match reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review P-Match