A Scoring System for Consensus Sequence Matching

• Activity Number: 528
• Type: Contributed
• Date/Time: Wednesday, August 1, 2012 : 10:30 AM to 12:20 PM
• Sponsor: WNAR
• Author(s): Dongseok Choi*+ and Kathryn Carr and Lauren Hayashi and Marry J Kelley and Ted Acott
• Companies: Oregon Health and Science University and Oregon Health and Science University and Oregon Health and Science University and Oregon Health and Science University and Oregon Health and Science University
• Keywords: transcription factor ; transcription factor binding site ; consensus sequence ; gene expression ; motif

Abstract

Transcription factors do serve a crucial role in regulating gene expression patterns. Transcription factor binding sites (TFBS) can be predicted from DNA base pair sequence data of a group of co-expressed genes using statistical models. Generally, a consensus sequence and matrix are returned from such analyses. A TFBS is about 8 -25 base pairs and the core sequence is about 5 base pairs. Although finding TFBS of a group of co-expressed genes is relatively straightforward due to the availability of software, identification is a challenge. One way to identify predicted TFBS is searching a database using a predicted consensus sequence. Unfortunately, database search usually returns multiple hits. In this presentation, a new method to rank multiple identifications will be presented.