Cited by 22,074Genomics and Phylogenetic StudiesAlgorithms and Data CompressionFractal and DNA sequence analysis

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BLAST+: architecture and applications

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Camacho, Christiam, Coulouris, George, Avagyan, Vahram, Ma, Ning, Papadopoulos, Jason, Bealer, Kevin, Madden, Thomas L·2009·BMC Bioinformatics

DOI 10.1186/1471-2105-10-421PMC PMC2803857

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Abstract

Background: Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST software is suboptimal for very long queries or database sequences. There are also some shortcomings in the user-interface of the current command-line applications. Results: We describe features and improvements of rewritten BLAST software and introduce new command-line applications. Long query sequences are broken into chunks for processing, in some cases leading to dramatically shorter run times. For long database sequences, it is possible to retrieve only the relevant parts of the sequence, reducing CPU time and memory usage for searches of short queries against databases of contigs or chromosomes. The program can now retrieve masking information for database sequences from the BLAST databases. A new modular software library can now access subject sequence data from arbitrary data sources. We introduce several new features, including strategy files that allow a user to save and reuse their favorite set of options. The strategy files can be uploaded to and downloaded from the NCBI BLAST web site. Conclusion: The new BLAST command-line applications, compared to the current BLAST tools, demonstrate substantial speed improvements for long queries as well as chromosome length database sequences. We have also improved the user interface of the command-line applications.

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Basic local alignment search tool
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Self-citation
Database indexing for production MegaBLAST searches
Morgulis, A. O., Coulouris, G., Raytselis, Y., Madden, T., Agarwala, R., & Schäffer, A. A. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn322 · Cited by 1,395
Self-citation
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements
Schäffer, A. A. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.14.2994 · Cited by 1,375
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Research works printed but not linked: 8

NCBI C toolkit[http://www.ncbi.nlm.nih.gov/IEB/ToolBox/SDKDOCS/INDEX.HTML]
NCBI BLAST web site[http://blast.ncbi.nlm.nih.gov/Blast.cgi]
NCBI C++ toolkit documentation[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=toolkit]
Implementing a BlastSeqSrc[http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/_impl_blast_seqsrc_howto.html]
BLAST+ Command Line Applications User Manual[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helpblast]
Reference assembly for Human genome build 36.1[http://www.ncbi.nlm.nih.gov/genome/guide/human/release_notes.html#b36]
NCBI SRA Software Development Kit[http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software]
PUBLIC DOMAIN NOTICE for NCBI[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=toolkit&part=toolkit.fm#A3]

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Authors: Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L.
Affiliations: National Institutes of Health (US)
Corresponding author: Madden, Thomas L
ORCID: Madden, Thomas L
Venue: BMC Bioinformatics
Publisher: Springer Science and Business Media LLC
Published: 2009-12
Volume: 10
Issue: 1
Pages: 421-421
ISSN: 1471-2105 (ISSN-L)
DOI: 10.1186/1471-2105-10-421
PMC: PMC2803857
OpenAlex: W2142678478
Cited by: 22,074
References: 15
Citations by year: 2026: 2652 · 2025: 2909 · 2024: 2584 · 2023: 2213 · 2022: 2114 · 2021: 2164 · 2020: 1780 · 2019: 1400 · 2018: 1093 · 2017: 979 · 2016: 725 · 2015: 518 · 2014: 412 · 2013: 241 · 2012: 144
FWCI: 36.21
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
Locations: BMC Bioinformatics (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders: National Institutes of Health
U.S. National Library of Medicine
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Physical Sciences › Mathematics › Theoretical Computer Science › Algorithms and Data Compression
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
Keywords: BLAST, sequence similarity searching, chunking, command-line tool, software performance optimization, user interface
MeSH terms: Software, Sequence Alignment, Computational Biology, Databases, Genetic

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