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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
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The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSI-BLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.
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“Fortunately, however, we do in fact have ready-to-use, well defined, and widely accepted stochastic models for the evolution of protein sequences.”
From On universal common ancestry, sequence similarity, and phylogenetic structure: the sins of P-values and the virtues of Bayesian evidence (2011) · cites this paper as [31]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
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“After initial gene predictions in each of the three sets of genomic scaffolds, we screened each set of gene models for internal redundancy with the BLASTP program from NCBI's BLAST 1 software suite 43 . A model was considered redundant if it: had 90% identity to other model; the alignment between the two models had a bit score of at least 100; and the model was shorter than the other model.”
From The ctenophore genome and the evolutionary origins of neural systems (2014) · cites this paper as [43]
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“The known mRNA sequences with full-length cds of sweet potato available in GenBank were considered as ‘gold standard’ reference in this study, and used to blast against each assembly by BLASTN [80].”
From Digital Gene Expression Analysis Based on Integrated De Novo Transcriptome Assembly of Sweet Potato [Ipomoea batatas (L.) Lam.] (2012) · cites this paper as [80]
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“A BLAST analysis (1) of GenBank indicated that amplification with these two oligonucleotides would only occur when a Plasmodium spp. was available to act as a template (expected value of 0.31 for both oligonucleotides).”
From Real-Time PCR for Detection and Identification of Plasmodium spp (2005) · cites this paper as [1]
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“The sequences obtained were compiled and compared to the sequences in the GenBank databases using BLAST analysis (Altschul et al. 1997).”
From Isolation and identification of high fluoride resistant bacteria from water samples of Dindigul district, Tamil Nadu, South India (2021) · cites this paper as Altschul et al. 1997
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“This means that the likelihood of a tree is not simply a function of the similarities of the sequences [31,101,102]. Rather, the likelihood of a phylogenetic tree is also a function of the nested pattern of similarities in the data.”
From On universal common ancestry, sequence similarity, and phylogenetic structure: the sins of P-values and the virtues of Bayesian evidence (2011) · cites this paper as [31]
Experimental — accuracy not yet measuredIn the citing paper
“The statistical significance of similarity between the TPase and RAG1s was measured by Ei = 0.025, where Ei is the E-value threshold for the first inclusion of RAG1 sequences into the PSI-BLAST iterations [18] (Materials and Methods).”
From RAG1 Core and V(D)J Recombination Signal Sequences Were Derived from Transib Transposons (2005) · cites this paper as [18]
In the citing paper
“A similarity search (Altschul et al. 1997) through the sequence data from C. albicans genome revealed two sequences, ORF19.2356 and ORF19.7359,showing high homology (score and probability values were 153 and 1e À37 , and 162 and 2e À40 , respectively) to the S. cerevisiae Crz1p transcription factor.”
From Functional characterization of the Candida albicans CRZ1 gene encoding a calcineurin-regulated transcription factor (2005) · cites this paper as Altschul et al. 1997
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“Protein BLAST analysis [25] of a 51 amino acid sequence comprising the last extra-cellular loop (from amino acid residue 531 to 581) exclusively returned known siderophore transporters and uncharacterized proteins predicted to encode fungal siderophore transporters”
From Host Iron Withholding Demands Siderophore Utilization for Candida glabrata to Survive Macrophage Killing (2011) · cites this paper as [25]
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Metadata
- Authors
- Altschul, S.
- Affiliations
- National Institutes of Health (US)
- Corresponding author
- Altschul, S.
- ORCID
- Altschul, S.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 1997-09-01
- Volume
- 25
- Issue
- 17
- Pages
- 3389-3402
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC146917
- OpenAlex
- W2158714788
- Cited by
- 73,302
- References
- 94
- Citations by year
- 2026: 1121 · 2025: 1665 · 2024: 1892 · 2023: 1802 · 2022: 2307 · 2021: 2555 · 2020: 2507 · 2019: 2405 · 2018: 2390 · 2017: 2358 · 2016: 2551 · 2015: 2748 · 2014: 3024 · 2013: 3230 · 2012: 3272
- FWCI
- 86.91
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nucleic Acids Research (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health (2r01lm005110-08)
- U.S. National Library of Medicine (LM05110)
- 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
- PSI-BLAST, sequence similarity
- MeSH terms
- Algorithms, Amino Acid Sequence, Animals, DNA, Humans, Molecular Sequence Data, Proteins, Software, Databases, Factual, Sequence Alignment
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