Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Open accessAbstract
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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Well-defined and widely accepted stochastic models for the evolution of protein sequences are available.
“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]
The Statistical Preliminaries section (page not available) describes a probabilistic model for random protein sequences and calls PAM and BLOSUM substitution matrices popular. It does not establish that these are ready-to-use stochastic models of protein-sequence evolution; the random-sequence model is used to assess alignment scores, not to describe evolution. (LLM, conf=0.76)
Experimental — accuracy not yet measuredAfter initial gene predictions, each set of gene models was screened for internal redundancy using BLASTP, with redundancy defined by 90% identity, bit score ≥100, and shorter length.
“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]
The known mRNA sequences with full-length cds of sweet potato available in GenBank were used as a 'gold standard' reference to evaluate the quality of the assemblies by BLASTN.
“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]
BLAST analysis indicated that amplification with the two oligonucleotides would only occur when a Plasmodium spp. was available to act as a template.
“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 <i>Plasmodium</i> spp (2005) · cites this paper as [1]
The likelihood of a phylogenetic tree is not simply a function of the similarities of the sequences; it is also a function of the nested pattern of similarities in the data.
“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]
The Sequence weights section discusses how related sequences affect alignment-based score matrices, not the likelihood of a phylogenetic tree. Searches for tree likelihood, topology, and nested patterns of similarity found no passage in our copy addressing the cited claim. (LLM, conf=0.76)
Experimental — accuracy not yet measured
The statistical significance of similarity between the Transib2_AG TPase and RAG1s was Ei = 0.025.
“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]
The C. albicans genome contains two sequences, ORF19.2356 and ORF19.7359, showing high homology to the S. cerevisiae Crz1p transcription factor.
“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
Protein BLAST analysis of a 51 amino acid sequence comprising last extra-cellular loop (residues 531 to 581) exclusively returned known siderophore transporters and uncharacterized proteins predicted to encode fungal siderophore transporters.
“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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Shifting the limits in wheat research and breeding using a fully annotated reference genome
Appels, R., Eversole, K., Stein, N., Feuillet, C., Keller, B., Rogers, J., Pozniak, C. J., Choulet, F., Distelfeld, A., Poland, J., et al. (2018) · Science · doi:10.1126/science.aar7191 · Cited by 3,107 · see citing works
MicroRNA targets in Drosophila
Enright, A. J., John, B., Gaul, U., Tuschl, T., Sander, C., & Marks, D. S. (2003) · Genome Biology · doi:10.1186/gb-2003-5-1-r1 · Cited by 3,597 · see citing works
Integrated Genomic Characterization of Papillary Thyroid Carcinoma
Agrawal, N., Akbani, R., Aksoy, B. A., Ally, A., Arachchi, H., Asa, S. L., Auman, J. T., Balasundaram, M., Balu, S., Baylin, S. B., et al. (2014) · Cell · doi:10.1016/j.cell.2014.09.050 · Cited by 3,080 · see citing works
- 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 › Computer Science › Artificial Intelligence › 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
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.
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