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          Institute: MPI für molekulare Genetik     Collection: Department of Computational Molecular Biology     Display Documents

ID: 27804.0, MPI für molekulare Genetik / Department of Computational Molecular Biology
Annotating regulatory DNA based on man-mouse genomic comparison
Authors:Dieterich, Christoph; Cusack, Brian; Wang, Haiyan; Rateitschak, Katja; Krause, Antje; Vingron, Martin
Date of Publication (YYYY-MM-DD):2002-06-15
Title of Journal:Bioinformatics
Volume:Supplement 2
Start Page:S84
End Page:S90
Title of Issue:Proceedings of the European Conference on Computational Biology (ECCB 2002)
Review Status:not specified
Audience:Experts Only
Abstract / Description:Non-coding DNA segments that are conserved between the human and mouse genomic sequence are good indicators of possible regulatory sequences. Here we report on a systematic approach to delineate such conserved elements from upstream regions of orthologous gene pairs from man and mouse. We focus on orthologous genes in order to maximize our chances to find functionally similar regulatory elements. The identification of conserved elements is effected using the Waterman–Eggert local suboptimal alignment algorithm. We have modified an implementation of this algorithm such that it integrates the determination of statistical significance for the local suboptimal alignments. This has the effect of outputting a dynamically determined number of suboptimal alignments that are deemed statistically significant. Comparison with experimentally determined annotation shows a striking enrichement of regulatory sites among the conserved regions. Furthermore, the conserved regions tend to cover the promotor region described in the EPD database.
External Publication Status:published
Document Type:Article
Communicated by:Martin Vingron
Affiliations:MPI für molekulare Genetik
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