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New EST Trimming Procedure Applied to SUCEST Sequences

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Advances in Bioinformatics and Computational Biology (BSB 2007)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 4643))

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Abstract

In order to improve EST trimming, we proposed a new method consisting of a new set of procedures to detect regions that do not belong to the sequenced organism or have low quality or low complexity. Most trimming procedures process ESTs in a pipeline where the output of an step is adopted as the input for the following one. In our method, all artifact detection steps process the raw EST and their results are combined in the last step, which outputs the trimmed sequence. This strategy reduces the occurrence of false negatives and, additionally, has the advantage of producing better artifact composition characterization for the analyzed sequences. We evaluated our method using SUCEST [1] ESTs. Based on the results, we concluded that our method suits projects that want to produce more reliable clusters.

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Authors and Affiliations

  1. Institute of Computing - Unicamp - Campinas - SP, Brazil

    Christian Baudet & Zanoni Dias

  2. Scylla Bioinformatics - Campinas - SP, Brasil

    Christian Baudet & Zanoni Dias

Authors
  1. Christian Baudet
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  2. Zanoni Dias
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Marie-France Sagot Maria Emilia M. T. Walter

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© 2007 Springer-Verlag Berlin Heidelberg

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Baudet, C., Dias, Z. (2007). New EST Trimming Procedure Applied to SUCEST Sequences. In: Sagot, MF., Walter, M.E.M.T. (eds) Advances in Bioinformatics and Computational Biology. BSB 2007. Lecture Notes in Computer Science(), vol 4643. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-73731-5_6

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  • DOI: https://doi.org/10.1007/978-3-540-73731-5_6

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-73730-8

  • Online ISBN: 978-3-540-73731-5

  • eBook Packages: Computer ScienceComputer Science (R0)

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