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A Method to Detect Gene Structure and Alternative Splice Sites by Agreeing ESTs to a Genomic Sequence

  • Paola Bonizzoni
  • Graziano Pesole
  • Raffaella Rizzi
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2812)

Abstract

In this paper we propose a new approach to the problem of predicting constitutive and alternative splicing sites by defining it as an optimization problem (MEFC). Then, we develop an algorithm to detect splicing sites based on the idea of using a combined analysis of a set of ESTs alignments to a genomic sequence instead of considering single EST alignments. In this way we require that all ESTs alignments must agree, i.e. are compatible to a plausible exon-intron structure of the genomic sequence. Indeed, we show that a progressive and independent alignment of ESTs may produce unsupported splicing forms. Our method has been implemented and experimental results show that it predicts alternative splicings with high accuracy and in a small amount of time. More precisely, compared to published splicing data, the method confirms validated data while in many cases it provides novel splicing forms supported by several ESTs alignments.

Keywords

Alternative Splice Splice Site Splice Form Alternative Splice Site Alternative Splice Form 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2003

Authors and Affiliations

  • Paola Bonizzoni
    • 1
  • Graziano Pesole
    • 2
  • Raffaella Rizzi
    • 1
  1. 1.Dipartimento di Informatica Sistemistica e ComunicazioneUniversità degli Studi di Milano – BicoccaMilanoItaly
  2. 2.Dipartimento di Scienze Biomolecolari e BiotecnologieUniversità degli Studi di MilanoMilanoItaly

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