High speed BLASTN: an accelerated MegaBLAST search tool
By Ying Chen, Weicai Ye, Yongdong Zhang, Yuesheng Xu. Nucleic Acids Research, 2015
614 citations recorded by the source corpus.
Sequence alignment is a long standing problem in bioinformatics. The Basic Local Alignment Search Tool (BLAST) is one of the most popular and fundamental alignment tools. The explosive growth of biological sequences calls for speedup of sequence alignment tools such as BLAST. To this end, we develop high speed BLASTN (HS-BLASTN), a parallel and fast nucleotide database search tool that accelerates MegaBLAST—the default module of NCBI-BLASTN. HS-BLASTN builds a new lookup table using the FMD-index of the database and employs an accurate and effective seeding method to find short stretches of identities (called seeds) between the query and the database. HS-BLASTN produces the same alignment results as MegaBLAST and its computational speed is much faster than MegaBLAST. Specifically, our experiments conducted on a 12-core server show that HS-BLASTN can be 22 times faster than MegaBLAST and exhibits better parallel performance than MegaBLAST. HS-BLASTN is written in C++ and the related source code is available at https://github.com/chenying2016/queries under the GPLv3 license.
Subfields: Artificial Intelligence, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/a6f739618adf920201f93932f28416ad36e92339
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Citations in the corpus
- An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography (2016, methodology): “To evaluate how informative different gene families are for estimation of abundance, we simulated 100 100-bp reads from each of the 112 gene families in each of the 5952 species and used HS-BLASTN (Chen et al. 2015) to map these reads back to a database that contained the full-length gene sequences.”
- MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis (2018, background): “…CONCOCT [19], MaxBin2 [20], metaBAT [21], CheckM [24], Binning_refiner [28], Kraken [29], Taxator-tk [30], BWA [32], SPAdes [34, 36], MegaHIT [35], KronaTools [37], Blobology [39], Mega-BLAST [45], TrimGalore [46], BMTagger [47], FastQC [48], Bowtie2 [49], Salmon [50, 51], and PROKKA [52].”