Pavesi Giulio, Mereghetti Paolo, Zambelli Federico, Stefani Marco, Mauri Giancarlo, Pesole Graziano
Dipartimento di Scienze Biomolecolari e Biotecnologie, University of Milano, Milano, Italy.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W566-70. doi: 10.1093/nar/gkl285.
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/.
理解在转录和转录后水平调控基因表达的复杂机制是后基因组时代最大的挑战之一。国防部（MOtif发现）工具网络服务器包含一组用于在核苷酸序列中发现新的保守序列和结构基序的工具，这些基序反过来又是调控活性的良好候选者。该服务器包括以下程序：Weeder，用于在共调控基因的核苷酸序列中发现保守的转录因子结合位点（TFBSs）；WeederH，用于在同源基因的序列中发现保守的TFBSs和远端调控模块；RNAProfile，用于在二级结构未知的未比对RNA序列中发现保守的二级结构基序。通过这种方式，可以将给定基因与其他共调控基因或其同源基因进行比较，或者可以分析其mRNA中调控其转录后命运的保守基序。因此，该网络服务器为研究人员提供了不同的策略和方法，以在转录和转录后水平研究基因表达的调控。可在http://www.pesolelab.it/modtools/和http://www.beacon.unimi.it/modtools/获取。
