title: MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes.
abstract: Understanding the complex mechanisms regulating gene expression at the transcriptional and post-transcriptional levels is one of the greatest challenges of the post-genomic era. The MoD (MOtif Discovery) Tools web server comprises a set of tools for the discovery of novel conserved sequence and structure motifs in nucleotide sequences, motifs that in turn are good candidates for regulatory activity. The server includes the following programs: Weeder, for the discovery of conserved transcription factor binding sites (TFBSs) in nucleotide sequences from co-regulated genes; WeederH, for the discovery of conserved TFBSs 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 with other co-regulated genes or with its homologs, or its mRNA can be analyzed for conserved motifs regulating its post-transcriptional fate. The web server thus provides researchers with different strategies and methods to investigate the regulation of gene expression, at both the transcriptional and post-transcriptional levels. Available at http://www.pesolelab.it/modtools/ and http://www.beacon.unimi.it/modtools/.
authors.affiliation: Dipartimento di Scienze Biomolecolari e Biotecnologie, University of Milano, Milano, Italy.
authors.forename: Giulio
authors.initials: G
authors.lastname: Pavesi
authors.forename: Paolo
authors.initials: P
authors.lastname: Mereghetti
authors.forename: Federico
authors.initials: F
authors.lastname: Zambelli
authors.forename: Marco
authors.initials: M
authors.lastname: Stefani
authors.forename: Giancarlo
authors.initials: G
authors.lastname: Mauri
authors.forename: Graziano
authors.initials: G
authors.lastname: Pesole
mesh_terms: D001665:Binding Sites; D005786:Gene Expression Regulation; D020407:Internet; D009690:Nucleic Acid Conformation; D022661:RNA, Untranslated / Q000737:chemistry; D050436:Regulatory Elements, Transcriptional; D038621:Regulatory Sequences, Ribonucleic Acid; D017422:Sequence Analysis, DNA / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*; D014584:User-Computer Interface
chemical_list: D022661:RNA, Untranslated; D038621:Regulatory Sequences, Ribonucleic Acid; D014157:Transcription Factors