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  Annotating regulatory DNA based on man-mouse genomic comparison

Dieterich, C., Cusack, B., Wang, H., Rateitschak, K., Krause, A., & Vingron, M. (2002). Annotating regulatory DNA based on man-mouse genomic comparison. Proceedings of the European Conference on Computational Biology (ECCB 2002), S84-S90.

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 Creators:
Dieterich, Christoph1, Author
Cusack, Brian2, Author              
Wang, Haiyan1, Author
Rateitschak, Katja1, Author
Krause, Antje1, Author
Vingron, Martin3, Author              
Affiliations:
1Max Planck Society, ou_persistent13              
2Evolutionary Genomics (Peter Arndt), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479638              
3Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479639              

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 Abstract: 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.

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Language(s): eng - English
 Dates: 2002-06-15
 Publication Status: Published in print
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 Identifiers: eDoc: 27804
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Title: Proceedings of the European Conference on Computational Biology (ECCB 2002)
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Pages: - Volume / Issue: - Sequence Number: - Start / End Page: S84 - S90 Identifier: -

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Title: Bioinformatics
Source Genre: Journal
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Pages: - Volume / Issue: Supplement 2 Sequence Number: - Start / End Page: - Identifier: -