mBLAST: Keeping up with the sequencing explosion for (meta)genome analysis.
Recent advances in next-generation sequencing technologies require alignment algorithms and software that can keep pace with the heightened data production. Standard algorithms, especially protein similarity searches, represent significant bottlenecks in analysis pipelines. For metagenomic approaches in particular, it is now often necessary to search hundreds of millions of sequence reads against large databases. Here we describe mBLAST, an accelerated search algorithm for translated and/or protein alignments to large datasets based on the Basic Local Alignment Search Tool (BLAST) and retaining the high sensitivity of BLAST. The mBLAST algorithms achieve substantial speed up over the National Center for Biotechnology Information (NCBI) programs BLASTX, TBLASTX and BLASTP for large datasets, allowing analysis within reasonable timeframes on standard computer architectures. In this article, the impact of mBLAST is demonstrated with sequences originating from the microbiota of healthy humans from the Human Microbiome Project. mBLAST is designed as a plug-in replacement for BLAST for any study that involves short-read sequences and includes high-throughput analysis. The mBLAST software is freely available to academic users at www.multicorewareinc.com.
MultiCoreWare, St. Louis, MO 63108, United States.
Curtis
C
Davis
The Genome Institute, Washington University, St. Louis, MO 63108, United States.
Karthik
K
Kota
MultiCoreWare, St. Louis, MO 63108, United States.
Venkat
V
Baldhandapani
MultiCoreWare, St. Louis, MO 63108, United States.
Wei
W
Gong
The Genome Institute, Washington University, St. Louis, MO 63108, United States.
Sahar
S
Abubucker
The Genome Institute, Washington University, St. Louis, MO 63108, United States.
Eric
E
Becker
The Genome Institute, Washington University, St. Louis, MO 63108, United States.
John
J
Martin
The Genome Institute, Washington University, St. Louis, MO 63108, United States.
Kristine M
KM
Wylie
Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
Radhika
R
Khetani
Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
Matthew E
ME
Hudson
The Genome Institute, Washington University, St. Louis, MO 63108, United States ; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, United States.
George M
GM
Weinstock
The Genome Institute, Washington University, St. Louis, MO 63108, United States ; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, United States ; Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63108, United States.
Makedonka
M
Mitreva
BLAST; acceleration; algorithm; mBLAST; performance; sequence alignments