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HSLS MolBio Available Software

Bioinformatics software available to Pitt researchers.

About TRANSFAC/Match

TRANSFAC is the database of eukaryotic transcription factors, their genomic binding sites, and DNA-binding profiles. Its library of positional weight matrices is a unique collection of DNA-binding models, suitable for a comprehensive analysis of genomic sequences for potential transcription factor binding sites.  The core of TRANSFAC comprises contents of two domains: One documents TF binding sites, usually in promoters or enhancers.  The other describes the binding proteins.

Key Features

  • Predict TF binding sites or composite elements within single DNA sequences with Match and CMsearch, using matrices (PWMs) from TRANSFAC or your own
  • Analyze microarray, ChIP-seq and RNA-seq data for over-represented TF-binding sites (FMatch/Step-by-step analysis)
  • Find de novo motifs in sequence sets with the DECOD algorithm and compare them against TRANSFAC matrices
  • Analyze gene sets for the presence of shared miRNA target sites
  • Build custom transcription regulatory networks from experimentally demonstrated factor-DNA and factor-factor interactions
  • Access detailed reports for transcription factors, their experimentally-characterized binding sites, regulated genes and promoters (with mapped regulatory features)
  • Download binding fragments from individual ChIP experiments in fasta or bed format, or lists of nearest genes, for analysis with FMatch or other tools.

Registration & Access Info

Register here

  • Must have Pitt email address
  • Web-based
  • Username/password required