Finding short DNA motifs using permuted Markov models
- Details
- Publication Year 2005-07,Volume 12,Issue #6,Page 894-906
- Journal Title
- JOURNAL OF COMPUTATIONAL BIOLOGY
- Publication Type
- Journal Article
- Abstract
- Many short DNA motifs, such as transcription factor binding sites (TFBS) and splice sites, exhibit strong local as well as nonlocal 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.
- Publisher
- MARY ANN LIEBERT INC
- Keywords
- SPLICE SITES; IDENTIFICATION; SEQUENCES; ALIGNMENT; SIGNALS; PREDICTION; GENES
- Publisher's Version
- https://doi.org/10.1089/cmb.2005.12.894
- Terms of Use/Rights Notice
- Refer to copyright notice on published article.
Creation Date: 2005-07-01 12:00:00