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Comment on "SCS: signal, context, and structure features for genome-wide human promoter recognition".

Authors
Type
Published Article
Journal
IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM
Publication Date
Volume
9
Issue
3
Pages
940–941
Identifiers
DOI: 10.1109/TCBB.2011.130
PMID: 21968958
Source
Medline

Abstract

We comment on the flexibility profiles calculated by Zeng et al., and show that these profiles do not represent the local flexibility of the DNA molecule. If one takes into account the physics of elasticity, the averaged flexibility profile show an additional peak which is missed in the original calculation. We show that it is not possible to calculate the flexibility of a 6-mer using tetranucleotide elastic constants, the shortest sequence is a 7-mer. For 6-mers, dinucleotide or trinucleotide parameters are needed. We present calculations for dinucleotide flexibility parameters and show that the same additional peak is present for both 7-mers and 6-mers.

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