Abstract
Background: Next Generation Sequencing (NGS) is producing enormous corpuses of short DNA reads, affecting emerging fields like metagenomics. Protein similarity search--a key step to achieve annotation of protein-coding genes in these short reads, and identification of their biological functions--faces daunting challenges because of the very sizes of the short read datasets.Results: We developed a fast protein similarity search tool RAPSearch that utilizes a reduced amino acid alphabet and suffix array to detect seeds of flexible length. For short reads (translated in 6 frames) we tested, RAPSearch achieved ~20-90 times speedup as compared to BLASTX. RAPSearch missed only a small fraction (~1.3-3.2%) of BLASTX similarity hits, but it also discovered additional homologous proteins (~0.3-2.1%) that BLASTX missed. By contrast, BLAT, a tool that is even slightly faster than RAPSearch, had significant loss of sensitivity as compared to RAPSearch and BLAST.Conclusions: RAPSearch is implemented as open-source software and is accessible at http://omics.informatics.indiana.edu/mg/RAPSearch. It enables faster protein similarity search. The application of RAPSearch in metageomics has also been demonstrated.
Original language | English (US) |
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Article number | 159 |
Journal | BMC Bioinformatics |
Volume | 12 |
DOIs | |
State | Published - May 15 2011 |
Externally published | Yes |
Keywords
- Metagenomics
- Reduced amino acid alphabet
- Short reads similarity search
- Suffix array
ASJC Scopus subject areas
- Structural Biology
- Biochemistry
- Molecular Biology
- Computer Science Applications
- Applied Mathematics