Search Transcription Factor Binding Motifs

• Tools for Discovery of Transcription Factor Binding Sites
  • AlignACE
    It is based on a Gibbs samplig algorithm and returns a series of motif as weight matrices that are overrepresented in the input set.
  • ANN-spec
    It uses a weight matrix to model the DNA-binding specificity of a transcription factor. The objective function is based on the log likelihood that a transcription factor binds at least once in each sequence of the positive training data compared to the number of times it is estimated to bind in the background training data.
  • Consensus
  • GLAM
  • Improbizer
  • MEME
  • MITRA
  • MotifSampler
  • Oligo/dyad-analysis
  • Quickscore
  • SeSiMCMC
  • Weeder
  • YMF
  • Cluster Buster
    Cluster-Buster finds clusters of pre-specified motifs in nucleotide sequences. The main application is detection of sequences that regulate gene transcription, such as enhancers and silencers, but other types of biologival regulation may be mediated by motif cluster too.
• Transcription Factor Binding Motifs Databases
  • Gene Regulation
    TRANSFAC, Patho DB, S/MARt DB, Cytomer, TRANSCompel, and TRANSPATH
  • Sequence Motif Search
    A web interface ported to TRANSFAC database.
  • SCPD, the Promoter Database of Saccharomyces cerevisiae
  • A Database on Transcriptional Regulation and Operon Organization in E. coli
  • Comparative Regulatory Genomics multi-species DNA comparison and annotation
• Yeast
  • Comprehensive Yeast Genome Database by MIPS
  • Saccharomyces Genome Database (SGD)
  • SGD Lite
  • yeast Microarray Global viewer
• Arabidopsis
  • Database of Arabidopsis Transcription Factors by PKU
  • The Arabdopsis Information Resource