Local combinational variables: an approach used in DNA-binding helix-turn-helix motif prediction with sequence information.

ABSTRACT: Sequence-based approach for motif prediction is of great interest and remains a challenge. In this work, we develop a local combinational variable approach for sequence-based helix-turn-helix (HTH) motif prediction. First we choose a sequence data set for 88 proteins of 22 amino acids in length to launch an optimized traversal for extracting local combinational segments (LCS) from the data set. Then after LCS refinement, local combinational variables (LCV) are generated to construct prediction models for HTH motifs. Prediction ability of LCV sets at different thresholds is calculated to settle a moderate threshold. The large data set we used comprises 13 HTH families, with 17 455 sequences in total. Our approach predicts HTH motifs more precisely using only primary protein sequence informa

SUBMITTER: Xiong W 

PROVIDER: S-EPMC2761287 | biostudies-literature | 2009 Sep

REPOSITORIES: biostudies-literature