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BLAST+: architecture and applications
Open accessAbstract
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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“In response to frequent requests from the user community since the AlphaFold DB launch, we have made significant strides to implement a sequence-based similarity search feature. We have incorporated the Basic Local Alignment Search Tool (BLAST) (21) into our Google Cloud Platform infrastructure to achieve this.”
From AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences (2024) · cites this paper as [21]
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“When searching the NR database using NCBI BLAST28, we found no bacterial hits for the human AIM2 gene.”
From Clustering predicted structures at the scale of the known protein universe (2023) · cites this paper as [28]
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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]
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- NCBI SRA Software Development Kit[http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software]
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Metadata
- 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
- Published
- 2009-12
- Volume
- 10
- Issue
- 1
- Pages
- 421-421
- ISSN
- 1471-2105 (ISSN-L)
- 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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