Format

Send to

Choose Destination
See comment in PubMed Commons below
Algorithms Mol Biol. 2006 May 19;1:8.

Analysis of computational approaches for motif discovery.

Author information

1
Department of Computer Science and Engineering, Box 352350, University of Washington, Seattle, WA 98195-2350, USA. annli@cs.washington.edu

Abstract

Recently, we performed an assessment of 13 popular computational tools for discovery of transcription factor binding sites (M. Tompa, N. Li, et al., "Assessing Computational Tools for the Discovery of Transcription Factor Binding Sites", Nature Biotechnology, Jan. 2005). This paper contains follow-up analysis of the assessment results, and raises and discusses some important issues concerning the state of the art in motif discovery methods: 1. We categorize the objective functions used by existing tools, and design experiments to evaluate whether any of these objective functions is the right one to optimize. 2. We examine various features of the data sets that were used in the assessment, such as sequence length and motif degeneracy, and identify which features make data sets hard for current motif discovery tools. 3. We identify an important feature that has not yet been used by existing tools and propose a new objective function that incorporates this feature.

PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for BioMed Central Icon for PubMed Central
    Loading ...
    Support Center