Title :
Parallel Discovery of Transcription Factor Binding Sites
Author :
Wirawan, Adrianto ; Schmidt, Bertil
Author_Institution :
Sch. of Comput. Eng., Nanyang Technol. Univ., Singapore
Abstract :
Transcription factor binding sites (TFBSs) are cis-acting control elements that regulate gene expression upon binding to their corresponding transcription factors (TFs). Genome wide discovery of transcription factor binding sites (TFBSs) would aid in understanding gene expression. Various experimental techniques are currently used for TFBS discovery, but are limited in scale and speed. Computational approaches have proven to be fast and reliable alternatives for discovering TFBS on a whole genome scale and offer several advantages to experimental techniques. However, algorithms for TFBS discovery are highly compute-intensive. This has so far limited their application to relatively small problem sizes. This paper presents the design of a parallel TFBS discovery algorithm. Its implementation on a high performance compute cluster leads to significant runtime savings
Keywords :
biology computing; biotechnology; genetics; cis-acting control elements; gene expression understanding; genome scale; parallel TFBS discovery; transcription factor binding sites; Bioinformatics; Clustering algorithms; Concurrent computing; Fungi; Gene expression; Genetic mutations; Genomics; Parallel algorithms; Runtime; Sequences;
Conference_Titel :
Circuits and Systems, 2006. APCCAS 2006. IEEE Asia Pacific Conference on
Conference_Location :
Singapore
Print_ISBN :
1-4244-0387-1
DOI :
10.1109/APCCAS.2006.342103