ConTra pipeline

ConTra specifications

Information


Unique identifier OMICS_09258
Name ConTra
Alternative name conserved TFBSs
Interface Web user interface
Restrictions to use None
Output data A list of PWMs for the exploration part and alignment blocks for the visualization part.
Programming languages Perl, R
Database management system MySQL
Computer skills Basic
Version 3
Stability Stable
Maintained Yes

Taxon


  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Mammals
    • Bos taurus
  • Plants and Fungi
    • Saccharomyces cerevisiae
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
  • Vertebrates
    • Danio rerio
    • Gallus gallus
    • Xenopus tropicalis

Documentation


Maintainer


  • person_outline Pieter De Bleser <>

Additional information


http://bioit2.irc.ugent.be/contra/v3/#/help

Publications for conserved TFBSs

ConTra IN pipelines

 (2)
2008
PMCID: 2267439
PMID: 18294369
DOI: 10.1186/1471-2105-9-112

[…] however, recently such tes have been reported to influence the gene regulatory network evolution. therefore, an alignment approach that is robust to te insertions is meaningful for finding novel conserved tfbss in tes., we constructed a web server 'realignerv' for complex alignment of genomic sequences. realignerv returns ladder-like schematic alignments that integrate predicted tfbss […]

2007
PMCID: 1803799
PMID: 17286865
DOI: 10.1186/1471-2105-8-46

[…] deriving from the usage of a single, global threshold of significance. these examples show how weederh can work at a much more fine grained level of detail, actually being able to identify correctly conserved tfbss either with little or, vice versa, a very high level of overall sequence conservation., given the difference in performance on the same threshold values for the artificial and real […]

ConTra institution(s)
VIB Bioinformatics Core, Zwijnaarde-Ghent, Belgium; VIB-UGent Center for Inflammation Research, Zwijnaarde-Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Zwijnaarde-Ghent, Belgium; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium

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