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- Title
Dinucleotide weight matrices for predicting transcription factor binding sites: generalizing the position weight matrix.
- Authors
Siddharthan, Rahul
- Abstract
Identifying transcription factor binding sites (TFBS) in silico is key in understanding gene regulation. TFBS are string patterns that exhibit some variability, commonly modelled as "position weight matrices" (PWMs). Though convenient, the PWM has significant limitations, in particular the assumed independence of positions within the binding motif; and predictions based on PWMs are usually not very specific to known functional sites. Analysis here on binding sites in yeast suggests that correlation of dinucleotides is not limited to near-neighbours, but can extend over considerable gaps.
- Publication
PloS one, 2010, Vol 5, Issue 3, pe9722
- ISSN
1932-6203
- Publication type
Journal Article
- DOI
10.1371/journal.pone.0009722