About LogoMotif

LogoMotif is an up-to-date comprehensive database for bacterial regulatory information, especially focusing on Actinobacteria. The database contains curated experimentally-validated transcription factor binding site (TFBS) profiles, which are stored in position frequency matrices (PFMs). In PFMs, the occurrence of each nucleotide at each position in an alignment of TFBS is counted. From the PFM, a position weight matrix (PWM) can be constructed, representing motifs in biological data. In LogoMotif, both the pre-calculated PFM and PWM are supplied, together with the visual representation in a sequence motif. These matrices can be used to scan a DNA sequence of interest for the presence of TFBSs. The database supplies predictions for several model organisms, using the TFBS detection algorithm MiniMotif.

What is in LogoMotif?

  • Experimentally validated TFBSs:
    • Reported binding sequences are collected from literature
  • Sequence motifs:
    • The collected binding sequences are represented as sequence motifs
    • Binding sequences are manually curated, assessing the quality and correctness of the motif
  • TFBS prediction:
    • PWMs and pHMMs are used to detect TFBSs
    • The prediction algorithms behind LogoMotif are available as commandline package: MiniMotif
    • TFBS detection in biosynthetic gene clusters (BGCs) is provided through the TFBS Finder option in prediction tool antiSMASH
  • Regulatory networks:
    • Networks are calculated based on the PWM and/or HMM results for several Streptomyces model organisms