Subject: | DNA motifs |
Presenter: | Sanja Rogic |
Paper: | " Finding short DNA motifs using permuted Markov models " |
  | by Xiaoyue Zhoa, Haiyan Huang, and Terence P. Speed |
Abstract |
Finding short DNA motifs using permuted Markov models
Many short DNA motifs such as transcription factor binding sites (TFBS)
and splice sites exhibit strong local as well as non-local dependence.
We introduce permuted variable length Markov models (PVLMM) which could
capture the potentially important dependencies among positions, and
apply them to the problem of detecting splice and TFB sites. They have
been satisfactory from the viewpoint of prediction performance, and also
give ready biological interpretations of the sequence dependence
observed. The issue of model selection is also studied.
Reference:
X. Zhoa, H. Huang, and T.P. Speed,
"Finding short DNA motifs using permuted Markov models", In RECOMB 2004
The paper is available at http://www.genetics.ucla.edu/home/seminar_files/speed-recomb2004.pdf
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