Combinatorial method of splice sites prediction

Alexander Churbanov, Hesham H Ali

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

3 Citations (Scopus)

Abstract

Predicting and proper ranking of splice sites (SS) is a challenging problem in bioinformatics and machine learning communities. Proposed method of donor and acceptor SSs prediction is based on counting oligonucleotide frequencies for splice and splice-like signals. Based on bayesian principle SS sensors were built. We demonstrate advantage of our proposed sensor design compared with existing sensors and tools. In particular, our donor sensor outperforms Maximum Entropy Sensor for several representative test sets of genes when compared on Receiver Operating Characteristic (ROC) curve. We represent combinatorial interaction of SSs and related factors with Logarithm Of oDds (LOD) weight matrices. Based on factor interactions we were able to substantially improve splice signals prediction quality and rank SSs better than SpliceView, GeneSplicer, NNSplice and Genio tools. Proposed method is used in our new splicing simulator SpliceScan.

Original languageEnglish (US)
Title of host publication2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts
Pages189-190
Number of pages2
DOIs
StatePublished - Dec 1 2005
Event2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts - Stanford, CA, United States
Duration: Aug 8 2005Aug 11 2005

Publication series

Name2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts

Conference

Conference2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts
CountryUnited States
CityStanford, CA
Period8/8/058/11/05

Fingerprint

Sensors
Oligonucleotides
Bioinformatics
Learning systems
Entropy
Genes
Simulators

ASJC Scopus subject areas

  • Engineering(all)

Cite this

Churbanov, A., & Ali, H. H. (2005). Combinatorial method of splice sites prediction. In 2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts (pp. 189-190). [1540593] (2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts). https://doi.org/10.1109/CSBW.2005.40

Combinatorial method of splice sites prediction. / Churbanov, Alexander; Ali, Hesham H.

2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts. 2005. p. 189-190 1540593 (2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts).

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

Churbanov, A & Ali, HH 2005, Combinatorial method of splice sites prediction. in 2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts., 1540593, 2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts, pp. 189-190, 2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts, Stanford, CA, United States, 8/8/05. https://doi.org/10.1109/CSBW.2005.40
Churbanov A, Ali HH. Combinatorial method of splice sites prediction. In 2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts. 2005. p. 189-190. 1540593. (2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts). https://doi.org/10.1109/CSBW.2005.40
Churbanov, Alexander ; Ali, Hesham H. / Combinatorial method of splice sites prediction. 2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts. 2005. pp. 189-190 (2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts).
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