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PatMatch specifications

Information


Unique identifier OMICS_29001
Name PatMatch
Interface Web user interface
Restrictions to use None
Input data A nucleotide or peptide sequence or pattern.
Programming languages Perl
Computer skills Basic
Version 1.1
Stability Stable
Maintained Yes

Taxon


  • Bacteria
    • Escherichia coli
  • Plants and Fungi
    • Arabidopsis thaliana

Maintainer


  • person_outline TAIR

Additional information


The web application is also available for Escherichia coli matching at: https://biocyc.org/patmatch.shtml?organism=ECOLI

Information


Unique identifier OMICS_29001
Name PatMatch
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format FASTA
Output data A file with each individual sequence on a single line.
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 1.2
Stability Stable
Maintained Yes

Taxon


  • Bacteria
    • Escherichia coli
  • Plants and Fungi
    • Arabidopsis thaliana

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Versioning


No version available

Maintainer


  • person_outline TAIR

Additional information


The web application is also available for Escherichia coli matching at: https://biocyc.org/patmatch.shtml?organism=ECOLI

Publication for PatMatch

PatMatch citations

 (54)
library_books

The Sequenced Angiosperm Genomes and Genome Databases

2018
Front Plant Sci
PMCID: 5909171
PMID: 29706973
DOI: 10.3389/fpls.2018.00418

[…] predicted gene interaction information, and has gained its popularity for the rapid development of metabolic and metabolomics researches. other tools include mapviewer, metabolic pathways, n-browse, patmatch, vxinsight, java tree view, bulk data retrieval, gene symbol registry, and textpresso full text. arapot (www.araport.org) is also an important arabidopsis genome database that provides […]

library_books

CIRCADIAN CLOCK ASSOCIATED 1 Inhibits Leaf Senescence in Arabidopsis

2018
Front Plant Sci
PMCID: 5845730
PMID: 29559987
DOI: 10.3389/fpls.2018.00280

[…] (cbs, aamaatct) and evening element (ee, aaaatatct) (). to examine whether circadian regulated cis-elements are enriched in the promoter regions of senescence-associated genes (sags), we used the patmatch tool on the tair website to search for cbs or ee in gene promoter regions (1000 bp sequence upstream of translation start site). according to the tair 10 genome background, 2330 genes […]

library_books

Identification and analysis of brown planthopper responsive microRNAs in resistant and susceptible rice plants

2017
Sci Rep
PMCID: 5562839
PMID: 28821824
DOI: 10.1038/s41598-017-09143-y

[…] a putative nbs-lrr disease resistance gene. we speculate that this may play an important role in the signal transduction of bph resistance.table 2 , to identify the target of these mirnas, we used patmatch software and predicted that 136 rice genes were the potential targets of the 23 differently expressed mirnas (table ). previous work suggests that the expression of a target gene […]

library_books

Sfp1 and Rtg3 reciprocally modulate carbon source‐conditional stress adaptation in the pathogenic yeast Candida albicans

2017
Mol Microbiol
PMCID: 5575477
PMID: 28574606
DOI: 10.1111/mmi.13722

[…] significant differences of the input cluster in comparison to the background gene database were considered if the e‐value was < 0.001. promoter analyses were performed via patmatch in the candida genome database. positive hits contained at least one identical match to the consensus sequence of interest within the 5′‐region of annotated c. albicans genes. graphs […]

library_books

The septin associated kinase Gin4 recruits Gps1 to the site of cell division

2017
Mol Biol Cell
PMCID: 5385937
PMID: 28148650
DOI: 10.1091/mbc.E16-09-0687

[…] suggest that multiple motifs are responsible for targeting gps1 to the bud neck before and after septin splitting. a genome-wide pattern search identified five proteins (www.yeastgenome.org/cgi-bin/patmatch/nph-patmatch; gps1, zds2, mso1, bpt1, and nth1) containing the rxxlxrsk sequence. three of these five proteins (gps1, zds2, and mso1) were reported to localize at the bud neck (; ). thus […]

library_books

Transcriptome Wide Identification, Classification, and Characterization of AP2/ERF Family Genes in the Desert Moss Syntrichia caninervis

2017
Front Plant Sci
PMCID: 5326779
PMID: 28289426
DOI: 10.3389/fpls.2017.00262

[…] () using the parameters: any number of repetitions per sequence, motif width ranges of 6–50 amino acids, and 11 as the maximum number of motif. the motif alignment was conducted using mast and patmatch programs (). physical and chemical characterization of genes with deduced amino acid sequence were analyzed using protparam and protein subcellular location(s) were predicted using psort. […]


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PatMatch institution(s)
Department of Plant Biology, Carnegie Institution of Washington, Stanford, CA, USA; Department of Computer Engineering, Santa Clara University, Santa Clara, CA, USA; National Center for Genome Resources, Santa Fe, NM, USA; Department of Genetics, Stanford University, Stanford, CA, USA
PatMatch funding source(s)
Supported, in part, by the National Science Foundation grant number DBI-9978564.

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