PatMatch statistics

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Citations per year

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

This map represents all the scientific publications referring to PatMatch per scientific context
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Protocols

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

Download


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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

 (17)
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

[…] targets is a putative NBS-LRR disease resistance gene. We speculate that this may play an important role in the signal transduction of BPH resistance. 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 should exhib […]

library_books

Curated protein information in the Saccharomyces genome database

2017
PMCID: 5467551
PMID: 28365727
DOI: 10.1093/database/bax011

[…] displayed as a peptide sequence with modified residues denoted by an asterisks or lowercase notation (; e.g. K.MSphosFSGYSPKPI.S). In these instances, SGD’s Pattern Matching tool (www.yeastgenome.org/patmatch; ) is utilized to determine and confirm the identity and position of the amino acid in the protein sequence that is modified, and in some cases, identify the protein itself. If there is any a […]

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

[…] rogram () 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. Mul […]

library_books

Identification of p53 target genes in Danio rerio

2016
Sci Rep
PMCID: 5007497
PMID: 27581768
DOI: 10.1038/srep32474

[…] p.ensembl.org/pub/release-79/fasta/danio_rerio/dna/), from which we retrieved the genomic coordinates of the genes and of the repeat/transposable elements.The pattern-matching tool initially used was PatMatch 1.2 (available at ftp://ftp.arabidopsis.org/home/tair/Software/). It implements an exact matching algorithm. It was run with this command line:perl patmatch.pl -n “RRRCWWGYYYN{0, 15}RRRCWWGYY […]

library_books

From one to many: expanding the Saccharomyces cerevisiae reference genome panel

2016
PMCID: 4795930
PMID: 26989152
DOI: 10.1093/database/baw020

[…] riants (). The automated annotations for the additional genomes, as produced by the AGAPE pipeline, have already been incorporated into SGD sequence and alignment pages, analysis tools such as BLAST, PatMatch, and the Variant Viewer, and are also available for download (). The application of manual curation to automated output improves the quality and increases the depth and granularity of genome […]

library_books

Arabidopsis Motif Scanner

2016
BMC Bioinformatics
PMCID: 4728824
PMID: 26817596
DOI: 10.1186/s12859-016-0896-x

[…] se limitations are overcome in AMS that consider intergenic region the portion of sequence between two coding sequences. Finally, AMS offers the option to use PWM for the input motif differently from PatMatch and RSAT.Most genes encode multiple transcripts by alternative promoters, alternative splicing, or alternative polyadenylation [–]. The combinatorial mechanism of alternative splicing increas […]


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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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