Title :
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
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;
Conference_Titel :
Biomedical Engineering and Informatics (BMEI), 2011 4th International Conference on
Conference_Location :
Shanghai
Print_ISBN :
978-1-4244-9351-7
DOI :
10.1109/BMEI.2011.6098717
