The DOI matches its Crossref record; 15 of the 15 references it cites were found in a registry or an index.
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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![Figure 2 Speedup of BLASTX searches for differently sized queries with and without query splitting. Different sized pieces of [Genbank:NC_007113.2] were searched against a set of human proteins. The query length in kbases is on the x-axis, with a log scale. On the y-axis is the fractional speedup, which is defined as (Tbaseline/Tblastx) - 1. Three searches were performed with both the baseline and the blastx applications (for each data point), and the lowest time for each application was used.](/paper-figures/5f6014a3c3104ec3ab94bb17d3808749/blast-architecture-and-applications-figure-2.jpg)
![Figure 3 L2 data cache misses for BLASTX searches with and without query splitting. Cache misses were measured by Cachegrind [24] and only misses reading from the cache are shown. On the x-axis are different query lengths in kbases. The number of L2 cache misses is shown on the y-axis. The top line is for the baseline application without query splitting, the bottom line is for the blastx application. The queries are different sized pieces of [Genbank:NC_007113.2] searched against the set of human proteins used for Figure 2.](/paper-figures/4c62c5c33b83407288eb5c66b3d3e3d2/blast-architecture-and-applications-figure-3.jpg)
![Figure 4 Scatter plot of MEGABLAST search times with and without partial retrieval. 163 human ESTs from UniGene cluster 235935 were searched against all human chromosomes [22]. On the x-axis are times for the baseline application; on the y-axis are times for the new blastn application. Sequences with the best improvement are those furthest to the right, and they also matched the largest number of subject sequences. A word size of 24 was used for the runs as well as database masking with RepeatMasker. Three searches were done with both the baseline and blastn application for each data point, and the lowest time for each application was used.](/paper-figures/a10e69ff70d44c0198dfc081a558d6f8/blast-architecture-and-applications-figure-4.jpg)
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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]
In the citing paper
“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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Self-citationDatabase indexing for production MegaBLAST searches
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[33] Analysis of compositionally biased regions in sequence databases
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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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- 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]
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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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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