Using enhancing signals to improve specificity of ab initio splice site sensors

Alexandre Tchourbanov, Hesham H Ali, Jitender S Deogun

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Citations (Scopus)

Abstract

In this paper, we describe a new approach to improve the precision of splice site annotation in human genes. The problem is known to be extremely challenging since the human splice signals are highly indistinct and frequent cryptic sites confuse signal sensors. There is a strong evidence that Exonic Splicing Enhancers (ESE) and Exonic Splicing Silencers (ESS) influence commitment to splicing at early stages. We propose the use of a Naïve Bayesian Network (BN) combined with Boltzmann machine splice sites sensor, to improve the specificity of splice site prediction. The SpliceScan program is implemented to demonstrate feasibility of specificity enhancement based on ESE/ESS signals interactions. SpliceScan is more sensitive than GeneSplicer and NNSplice for the same specificity. The designed method is of particular value for ab initio gene annotation.

Original languageEnglish (US)
Title of host publicationProceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004
Pages672-673
Number of pages2
StatePublished - Dec 1 2004
EventProceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004 - Stanford, CA, United States
Duration: Aug 16 2004Aug 19 2004

Publication series

NameProceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004

Conference

ConferenceProceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004
CountryUnited States
CityStanford, CA
Period8/16/048/19/04

Fingerprint

Genes
Sensors
Bayesian networks

Keywords

  • Ab initio methods
  • Acceptor
  • Donor
  • Splicing enhancer
  • Splicing silencer

ASJC Scopus subject areas

  • Engineering(all)

Cite this

Tchourbanov, A., Ali, H. H., & Deogun, J. S. (2004). Using enhancing signals to improve specificity of ab initio splice site sensors. In Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004 (pp. 672-673). (Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004).

Using enhancing signals to improve specificity of ab initio splice site sensors. / Tchourbanov, Alexandre; Ali, Hesham H; Deogun, Jitender S.

Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004. 2004. p. 672-673 (Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Tchourbanov, A, Ali, HH & Deogun, JS 2004, Using enhancing signals to improve specificity of ab initio splice site sensors. in Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004. Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004, pp. 672-673, Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004, Stanford, CA, United States, 8/16/04.
Tchourbanov A, Ali HH, Deogun JS. Using enhancing signals to improve specificity of ab initio splice site sensors. In Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004. 2004. p. 672-673. (Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004).
Tchourbanov, Alexandre ; Ali, Hesham H ; Deogun, Jitender S. / Using enhancing signals to improve specificity of ab initio splice site sensors. Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004. 2004. pp. 672-673 (Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004).
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