BITS Meetings' Virtual Library:
Abstracts from Italian Bioinformatics Meetings from 1999 to 2013

766 abstracts overall from 11 distinct proceedings

1. Pavesi G, Mauri G, Pesole G
Weeder Web: a Web-Based Tool for the Discovery of Transcription Factor Binding Sites
Meeting: BITS 2004 - Year: 2004
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Topic: Comparative genomics

Abstract: Understanding the complex mechanisms governing basic biological processes requires the characterization of regulatory motifs modulating gene expression at transcriptional and post-transcriptional level. In particular, the extent, chronology and cell-specificity of transcription are modulated by the interaction of transcription factors (TFs) with their corresponding binding sites (TFBS), located in the promoter regions of the genes. The ever growing amount of genomic data, complemented by other sources of information concerning gene expression opens new opportunities to researchers. Transcription factor binding sites are generally short (less than 12-14 bp long) and degenerate oligonucleotides, and this fact makes significantly harder their computational discovery and large-scale annotation. Hence, the need for efficient and reliable methods for detecting novel motifs, significantly over-represented in the regulatory regions of sets of genes sharing common properties (e.g. similar expression profile, biological function, product cellular localization, etc.), that in turn could represent binding sites for the some common TF regulating the genes. We present here a Web server that provides access to a previously developed enumerative pattern discovery method [1] that is able to carry out an exhaustive search of significantly conserved degenerate oligonucleotide patterns with remarkable computational efficiency. Also, the interface has been designed in order avoid the explicit definition of a large number of parameters that were included in the original general-case implementation of the algorithm, as well as to produce a simpler “user-friendly” output. The parameters have been set to default values suitable for capturing TFBSs. The interface Web address is:

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