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Popular tool citations

chevron_left Motif discovery Bioinformatics workflows ChIP-seq data visualization Peak clustering chevron_right
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Associated diseases

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Trawler specifications

Information


Unique identifier OMICS_06287
Name Trawler
Alternative names TrawlerWeb, trawler_standalone
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl
License BSD 3-clause “New” or “Revised” License, MIT License
Computer skills Advanced
Version 1.2
Stability Stable
Requirements
Java, Ghostscript, Algorithm-Cluster
Maintained Yes

Taxon


  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Plants and Fungi
    • Arabidopsis thaliana
    • Saccharomyces cerevisiae
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus
  • Vertebrates
    • Danio rerio
    • Gallus gallus
    • Xenopus tropicalis

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Documentation


Maintainers


  • person_outline Benedict Paten <>
  • person_outline Mirana Ramialison <>
  • person_outline Laurence Ettwiller <>
  • person_outline Yannick Haudry <>

Information


Unique identifier OMICS_06287
Name Trawler
Alternative names TrawlerWeb, trawler_standalone
Interface Web user interface
Restrictions to use None
Input format BED,FASTA
Programming languages Java, Perl
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Plants and Fungi
    • Arabidopsis thaliana
    • Saccharomyces cerevisiae
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus
  • Vertebrates
    • Danio rerio
    • Gallus gallus
    • Xenopus tropicalis

Documentation


Maintainers


  • person_outline Benedict Paten <>
  • person_outline Mirana Ramialison <>
  • person_outline Laurence Ettwiller <>
  • person_outline Yannick Haudry <>

Publications for Trawler

Trawler in publications

 (5)
PMCID: 4548209
PMID: 26146939
DOI: 10.7554/eLife.06942.032

[…] on the affymetrix microarrays. the whole genome was used as background with david., de novo motif analysis of tf-binding sites was performed using the stand-alone version of weeder 1.4.2 () and trawler_standalone (). parameters for running weeder were: search mode=small-medium. parameters for running trawler_standalone were: motif_number=200-1000; mlength=6-12; wildcard=23; strand=double; […]

PMCID: 4265420
PMID: 25442502
DOI: 10.1186/1471-2164-15-1047

[…] of cres need to be identified by a motif-finding tool [, ]. although a few new motif-finders have been developed to analyze large sequence sets from chip-seq experiments, such as seeder [], trawler [, ], chipmunk [], hms [], cmf [], steme [], dreme [], decod [], rsat [], and posmo [], they are typically used to find the cres of a chip-ed tf in a short region of sequences (~200 bp) […]

PMCID: 3603212
PMID: 22517426
DOI: 10.1093/bib/bbs016

[…] complexity both in theory and in practice., all these considerations have thus led to the introduction of consensus-based methods tailored for working on large scale chip studies, like mdscan [], trawler [], amadeus [] (introduced for chip on chip), and dreme [], cisfinder [], cermit [], hms [], and rsat peak-motifs [] (introduced for chip-seq). all these tools report significant reduction […]

PMCID: 3214047
PMID: 22096565
DOI: 10.1371/journal.pone.0027384

[…] other interpretations are possible ., to identify the characteristics of the cis-regulatory motifs over-represented in the set of irf8-bound targets, repeat-masked chip sequences were queried in trawler . two over-represented position weight matrices were generated by comparison to human 1000 bp upstream genome sequences as a background (). the top matrix (z score = 22.99) contains two […]

PMCID: 3171486
PMID: 21931761
DOI: 10.1371/journal.pone.0024576

[…] numerous de novo motif discovery tools have been recently developed and quickly adapted by investigators in the community, including alignace , reduce , meme , ymf , mdscan , weeder , dme and trawler . despite these available tools, the effective and efficient identification of motifs within datasets of interest remains a challenging problem, particularly when studying datasets derived […]


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Trawler institution(s)
Australian Regenerative Medicine Institute, Systems Biology Institute Australia, Monash University, Clayton, VIC, Australia; eResearch, Monash University, Clayton, VIC, Australia; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA; Department of Biochemistry and Molecular Biology, Bio21 Institute and Cell Signalling Research Laboratories, The University of Melbourne, Melbourne, VIC, Australia; CNRS, Inserm, Institute of Biology Valrose, Université Côte d’Azur, Nice, France; School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia; Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Monash University, Clayton, VIC, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Faculty of Information Technology, Monash University, Clayton, VIC, Australia; Murdoch Children’s Research Institute, The Royal Children’s Hospital, Parkville, VIC, Australia; Department of Physiology, School of Biomedical Sciences, The University of Melbourne, Parkville, VIC, Australia
Trawler funding source(s)
Supported by an Australian Research Council Discovery Project grant (DP1049980), a National Health and Medical Research Council/ Heart Foundation Career Development Fellowship (1049980), Sun Foundation and UROP scholarships.

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