GeneExpress: A Computer System for Description, Analysis, and Recognition of Regulatory Sequences in Eukaryotic Genome

Nikolay Kolchanov, Mikhail Ponomarenko, Alexander Kel, Yury Kondrakhin, Anatoly Frolov, Fedor Kolpakov, Tatyana Goryachkovsky, Olga Kel, Elena Ananko, Elena Ignatieva, Olga Podkolodnaya, Vladimir. Babenko, Irina Stepanenko, Ada Romashchenko, Tatyana Merkulova, Denis Vorobiev, Sergey Lavryushev, Yulia Ponomarenko, Alexay Kochetov, Gregory Kolesov, Victor Solovyev, Luciano Milanesi, Nikolay Podkolodny, Edgar Wingender, and Thomas Heinemeyer

GeneExpress system has been designed to integrate description, analysis, and recognition of eukaryotic regulatory sequences. The system includes 5 basic units: (1) GeneNet contains an object-oriented database for accumulation of data on gene networks and signal transduction pathways and a Java-based viewer that allows an exploration and visualization of the GeneNet information; (2) Transcription Regulation combines the database on transcription regulatory regions of eukaryotic genes (TRRD) and TRRD Viewer; (3) Transcription Factor Binding Site Recognition contains a compilation of transcription factor binding sites (TFBSC) and programs for their analysis and recognition; (4) mRNA Translation is designed for analysis of structural and contextual features of mRNA 5'UTRs and prediction of their translation efficiency; and (5) ACTIVITY is the module for analysis and site activity prediction of a given nucleotide sequence. Integration of the databases in the GeneExpress is based on the Sequence Retrieval System (SRS) created in the European Bioinformatics Institute.

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