Computational Tools for the Discovery of Regulatory Elements in Nucleotide Sequences from Co-Regulated or Homologous Genes

The MoD (MOtif Discovery) Tools web server comprises a set of computational tools for the discovery of novel conserved sequence and structure motifs in nucleotide sequences, motifs that in turn are good candidates for regulatory activity. More in detail, the server includes the following programs: Weeder, for the discovery of conserved transcription factor binding sites in nucleotide sequences from co-regulated genes; WeederH, for the discovery of conserved transcription factor binding sites and distal regulatory modules in sequences from homologous genes; RNAProfile, for the discovery of conserved secondary structure motifs in unaligned RNA sequences whose secondary structure is not known. In this way, a given gene can be compared to other co-regulated genes, or to its homologs, or its mRNA can be analyzed looking for conserved motifs regulating its post-transcriptional fate.