A study of n-gram and decision tree letter language modeling methods
Speech Communication
Modeling dependencies in protein-DNA binding sites
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
The minimum description length principle in coding and modeling
IEEE Transactions on Information Theory
DNA Motif Representation with Nucleotide Dependency
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Journal of Biomedical Informatics
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
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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.