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

Alexandre Tchourbanov; Hesham H. Ali; Jitender Deogun

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

Alexandre Tchourbanov, Hesham H. Ali, Jitender Deogun

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

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 language	English (US)
Title of host publication	Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004
Pages	672-673
Number of pages	2
State	Published - 2004
Event	Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004 - Stanford, CA, United States Duration: Aug 16 2004 → Aug 19 2004

Publication series

Name	Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004

Conference

Conference	Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004
Country/Territory	United States
City	Stanford, CA
Period	8/16/04 → 8/19/04

Keywords

Ab initio methods
Acceptor
Donor
Splicing enhancer
Splicing silencer

ASJC Scopus subject areas

General Engineering

Cite this

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

Tchourbanov, A, Ali, HH & Deogun, J 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.

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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 Na{\"i}ve 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.",

keywords = "Ab initio methods, Acceptor, Donor, Splicing enhancer, Splicing silencer",

author = "Alexandre Tchourbanov and Ali, {Hesham H.} and Jitender Deogun",

year = "2004",

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series = "Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004",

pages = "672--673",

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note = "Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004 ; Conference date: 16-08-2004 Through 19-08-2004",

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T1 - Using enhancing signals to improve specificity of ab initio splice site sensors

AU - Tchourbanov, Alexandre

AU - Ali, Hesham H.

AU - Deogun, Jitender

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Y1 - 2004

N2 - 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.

AB - 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.

KW - Ab initio methods

KW - Acceptor

KW - Donor

KW - Splicing enhancer

KW - Splicing silencer

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T3 - Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004

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BT - Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004

T2 - Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004

Y2 - 16 August 2004 through 19 August 2004

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

Abstract

Publication series

Conference

Keywords

ASJC Scopus subject areas

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