Extracting DNA words based on the sequence features: non-uniform distribution and integrity.

ABSTRACT:

Background

DNA sequence can be viewed as an unknown language with words as its functional units. Given that most sequence alignment algorithms such as the motif discovery algorithms depend on the quality of background information about sequences, it is necessary to develop an ab initio algorithm for extracting the "words" based only on the DNA sequences.

Methods

We considered that non-uniform distribution and integrity were two important features of a word, based on which we developed an ab initio algorithm to extract "DNA words" that have potential functional meaning. A Kolmogorov-Smirnov test was used for consistency test of uniform distribution of DNA sequences, and the integrity was judged by the sequence and position alignment. Two random base sequences were adopted as

SUBMITTER: Li Z 

PROVIDER: S-EPMC4727310 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature