TY - GEN
T1 - Combinatorial method of splice sites prediction
AU - Churbanov, Alexander
AU - Ali, Hesham
PY - 2005
Y1 - 2005
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=33749063198&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=33749063198&partnerID=8YFLogxK
U2 - 10.1109/CSBW.2005.40
DO - 10.1109/CSBW.2005.40
M3 - Conference contribution
AN - SCOPUS:33749063198
SN - 0769524427
SN - 9780769524429
T3 - 2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts
SP - 189
EP - 190
BT - 2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts
T2 - 2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts
Y2 - 8 August 2005 through 11 August 2005
ER -