bCloudBLAST: An efficient mapreduce program for bioinformatics applications

Author

Meng, Zhen ; Li, Jianhui ; Zhou, Yunchun ; Liu, Qi ; Liu, Yong ; Cao, Wei

Author_Institution

Sci. Data Center, Comput. Network Inf. Center, Beijing, China

Volume

4

fYear

2011

fDate

15-17 Oct. 2011

Firstpage

2072

Lastpage

2076

Abstract

The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. We present an improved MapReduce-parallel implementation by splitting both of input query sequence files and sequence databases for search, called bCloudBLAST, showing very good scaling and speedup behavior on large sequence database. bCloudBLAST is written in Java, executable on UNIX/Linux, Windows and NacOS systems. (Free) MapReduce and Hadoop libraries can be found at http://hadoop.apache.org/. For download: http://www.darwintree.cn/tools.htm.

Keywords

DNA; Java; Linux; bioinformatics; molecular biophysics; molecular configurations; parallel databases; proteins; query processing; DNA databases; Hadoop libraries; Java; Linux; MapReduce program; NacOS systems; UNIX; Windows; bCloudBLAST; bioinformatics; input query sequence files; parallel implementation; protein databases; sequence databases; sequence similarities; Bioinformatics; Computer architecture; Databases; Phylogeny; Protein sequence; Virtual machining; BLAST; Bioinformatics; Cloud computing; MapReduce; bCloudBLAST;

fLanguage

English

Publisher

ieee

Conference_Titel

Biomedical Engineering and Informatics (BMEI), 2011 4th International Conference on

Conference_Location

Shanghai

Print_ISBN

978-1-4244-9351-7

Type

conf

DOI

10.1109/BMEI.2011.6098717

Filename

6098717