TY - GEN
T1 - A genome signature based on Markov modeling
AU - Li, Jian
AU - Sayood, Khalid
PY - 2005
Y1 - 2005
N2 - We propose a "genome signature" for bacterial genomes based on a triplets Markov model. Without the alignment or data preprocessing required by traditional analysis methods, the model is shown to efficiently capture identifying genomic information at both species and strain levels. Based on the model, a simple assumption-free distance measure is proposed for constructing phytogeny trees. The approach avoids problems with word frequency approaches such as balancing word length and window size. The method is shown to work successfully with both bacterial whole genome data and individual eukaryotic genes. Application of the model to phylogenetic analysis is presented.
AB - We propose a "genome signature" for bacterial genomes based on a triplets Markov model. Without the alignment or data preprocessing required by traditional analysis methods, the model is shown to efficiently capture identifying genomic information at both species and strain levels. Based on the model, a simple assumption-free distance measure is proposed for constructing phytogeny trees. The approach avoids problems with word frequency approaches such as balancing word length and window size. The method is shown to work successfully with both bacterial whole genome data and individual eukaryotic genes. Application of the model to phylogenetic analysis is presented.
UR - http://www.scopus.com/inward/record.url?scp=33947132099&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=33947132099&partnerID=8YFLogxK
M3 - Conference contribution
AN - SCOPUS:33947132099
SN - 0780392329
SN - 9780780392328
T3 - 2005 IEEE International Conference on Electro Information Technology
BT - 2005 IEEE International Conference on Electro Information Technology
T2 - 2005 IEEE International Conference on Electro Information Technology
Y2 - 22 May 2005 through 25 May 2005
ER -