Cited by 4,232

The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.

NCBI BLAST: a better web interface

Open access

Johnson, M., Zaretskaya, I., Raytselis, Y., Merezhuk, Y., McGinnis, S., Madden, T. L.·2008·Nucleic Acids Research

Open this paper in CoChat — free account

Abstract

Basic Local Alignment Search Tool (BLAST) is a sequence similarity search program. The public interface of BLAST, http://www.ncbi.nlm.nih.gov/blast, at the NCBI website has recently been reengineered to improve usability and performance. Key new features include simplified search forms, improved navigation, a list of recent BLAST results, saved search strategies and a documentation directory. Here, we describe the BLAST web application's new features, explain design decisions and outline plans for future improvement.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1093/nar/gkn201

Cites

2 of 2 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302

Show all 2 references

Research works printed but not linked: 5

1991, Methods (San Diego, Calif.), 3, 66, 10.1016/S1046-2023(05)80165-3 · DOI
Altschul, 2005, FEBS Journal, 272, 5101, 10.1111/j.1742-4658.2005.04945.x · DOI
Altschul, 1991, Journal of molecular biology, 219, 555, 10.1016/0022-2836(91)90193-A · DOI
McGinnis, 2004, Nucleic Acids Research, 32, W20, 10.1093/nar/gnh003 · DOI · Paper page
Ye, 2006, Nucleic Acids Research, 34, W6, 10.1093/nar/gkl164 · DOI · Paper page

BLAST+: architecture and applications
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-421 · Cited by 22,074
Self-citation
GenBank
Benson, D. A., Cavanaugh, M., Clark, K., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., & Sayers, E. W. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1195 · Cited by 3,261
Dominant and diet-responsive groups of bacteria within the human colonic microbiota
Walker, A. W., Ince, J., Duncan, S. H., Webster, L. M., Holtrop, G., Ze, X., Brown, D., Stares, M. D., Scott, P., Bergerat, A., et al. (2011) · The ISME Journal · doi:10.1038/ismej.2010.118 · Cited by 1,632
BLAST: a more efficient report with usability improvements
Boratyn, G. M., Camacho, C., Cooper, P. S., Coulouris, G., Fong, A., Ma, N., Madden, T. L., Matten, W. T., McGinnis, S. D., Merezhuk, Y., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt282 · Cited by 1,369
Self-citation
Human placenta has no microbiome but can contain potential pathogens
de Goffau, M. C., Lager, S., Sovio, U., Gaccioli, F., Cook, E., Peacock, S. J., Parkhill, J., Charnock-Jones, D. S., & Smith, G. C. S. (2019) · Nature · doi:10.1038/s41586-019-1451-5 · Cited by 691
Giving structure to the biofilm matrix: an overview of individual strategies and emerging common themes
Hobley, L., Harkins, C., MacPhee, C. E., & Stanley-Wall, N. R. (2015) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuv015 · Cited by 581
SARS-CoV-2-derived peptides define heterologous and COVID-19-induced T cell recognition
Nelde, A., Bilich, T., Heitmann, J. S., Maringer, Y., Salih, H. R., Roerden, M., Lübke, M., Bauer, J., Rieth, J., Wacker, M., et al. (2021) · Nature Immunology · doi:10.1038/s41590-020-00808-x · Cited by 582
High prevalence of Streptococcus pyogenes Cas9-reactive T cells within the adult human population
Wagner, D. L., Amini, L., Wendering, D. J., Burkhardt, L.-M., Akyüz, L., Reinke, P., Volk, H.-D., & Schmueck-Henneresse, M. (2019) · Nature Medicine · doi:10.1038/s41591-018-0204-6 · Cited by 399
Lower Airway Dysbiosis Affects Lung Cancer Progression
Tsay, J.-C. J., Wu, B. G., Sulaiman, I., Gershner, K., Schluger, R., Li, Y., Yie, T.-A., Meyn, P., Olsen, E., Perez, L., et al. (2021) · Cancer Discovery · doi:10.1158/2159-8290.cd-20-0263 · Cited by 322
Discovery of deaminase functions by structure-based protein clustering
(2023) · doi:10.1016/j.cell.2023.05.041 · Cited by 240
The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping
Beresford-Jones, B. S., Forster, S. C., Stares, M. D., Notley, G., Viciani, E., Browne, H. P., Boehmler, D. J., Soderholm, A. T., Kumar, N., Vervier, K., et al. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2021.12.003 · Cited by 194
Evolution combined with genomic study elucidates genetic bases of isobutanol tolerance in Escherichia coli
Minty, J. J., Lesnefsky, A. A., Lin, F., Chen, Y., Zaroff, T. A., Veloso, A. B., Xie, B., McConnell, C. A., Ward, R. J., Schwartz, D. R., et al. (2011) · Microbial Cell Factories · doi:10.1186/1475-2859-10-18 · Cited by 185
Discovery of phage determinants that confer sensitivity to bacterial immune systems
Stokar-Avihail, A., Fedorenko, T., Hör, J., Garb, J., Leavitt, A., Millman, A., Shulman, G., Wojtania, N., Melamed, S., Amitai, G., et al. (2023) · Cell · doi:10.1016/j.cell.2023.02.029 · Cited by 176
Protein generation with evolutionary diffusion: sequence is all you need
Alamdari, S., Thakkar, N., van den Berg, R., Tenenholtz, N., Strome, R., Moses, A. M., Lu, A. X., Fusi, N., Amini, A. P., & Yang, K. K. (2023) · doi:10.1101/2023.09.11.556673 · Cited by 154
A Novel Angiotensin II–Induced Long Noncoding RNA Giver Regulates Oxidative Stress, Inflammation, and Proliferation in Vascular Smooth Muscle Cells
Das, S., Zhang, E., Senapati, P., Amaram, V., Reddy, M. A., Stapleton, K., Leung, A., Lanting, L., Wang, M., Chen, Z., et al. (2018) · Circulation Research · doi:10.1161/circresaha.118.313207 · Cited by 141
Global analysis of shared T cell specificities in human non-small cell lung cancer enables HLA inference and antigen discovery
Chiou, S.-H., Tseng, D., Reuben, A., Mallajosyula, V., Molina, I. S., Conley, S., Wilhelmy, J., McSween, A. M., Yang, X., Nishimiya, D., et al. (2021) · Immunity · doi:10.1016/j.immuni.2021.02.014 · Cited by 133
Adrenal Mitochondria and Steroidogenesis: From Individual Proteins to Functional Protein Assemblies
Midzak, A., & Papadopoulos, V. (2016) · Frontiers in Endocrinology · doi:10.3389/fendo.2016.00106 · Cited by 114
“CYP11B3, CYP24A1, CYP27A1, CYP27B1, and CYP27C1) were identified using the nucleotide BLAST tool (41).”
Method
The Bacteriology of Pouchitis: A Molecular Phylogenetic Analysis Using 16S rRNA Gene Cloning and Sequencing
McLaughlin, S. D., Walker, A. W., Churcher, C., Clark, S. K., Tekkis, P. P., Johnson, M. W., Parkhill, J., Ciclitira, P. J., Dougan, G., Nicholls, R. J., et al. (2010) · Annals of Surgery · doi:10.1097/sla.0b013e3181e3dc8b · Cited by 114
Self-citation
Genetic interactions reveal the evolutionary trajectories of duplicate genes
VanderSluis, B., Bellay, J., Musso, G., Costanzo, M., Papp, B., Vizeacoumar, F. J., Baryshnikova, A., Andrews, B., Boone, C., & Myers, C. L. (2010) · Molecular Systems Biology · doi:10.1038/msb.2010.82 · Cited by 110
A topological approach for protein classification
Cang, Z., Mu, L., Wu, K., Opron, K., Xia, K., & Wei, G.-W. (2015) · Computational and Mathematical Biophysics · doi:10.1515/mlbmb-2015-0009 · Cited by 93
The cold-induced transcription factor bHLH112 promotes artemisinin biosynthesis indirectly via ERF1 in Artemisia annua
Xiang, L., Jian, D., Zhang, F., Yang, C., Bai, G., Lan, X., Chen, M., Tang, K., & Liao, Z. (2019) · Journal of Experimental Botany · doi:10.1093/jxb/erz220 · Cited by 84
De novo-designed pMHC binders facilitate T cell–mediated cytotoxicity toward cancer cells
Johansen, K. H., Wolff, D. S., Scapolo, B., Fernández-Quintero, M. L., Risager Christensen, C., Loeffler, J. R., Rivera-de-Torre, E., Overath, M. D., Kjærgaard Munk, K., Morell, O., et al. (2025) · Science · doi:10.1126/science.adv0422 · Cited by 77
Identifying B-cell epitopes using AlphaFold2 predicted structures and pretrained language model
Zeng, Y., Wei, Z., Yuan, Q., Chen, S., Yu, W., Lu, Y., Gao, J., & Yang, Y. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btad187 · Cited by 73
Why species delimitation matters for fungal ecology: Colletotrichum diversity on wild and cultivated cashew in Brazil
Veloso, J. S., Câmara, M. P. S., Lima, W. G., Michereff, S. J., & Doyle, V. P. (2018) · Fungal Biology · doi:10.1016/j.funbio.2018.03.005 · Cited by 65
Quorum-sensing synthase mutations re-calibrate autoinducer concentrations in clinical isolates of Pseudomonas aeruginosa to enhance pathogenesis
(2023) · doi:10.1038/s41467-023-43702-4 · Cited by 55
Aberrant methylmalonylation underlies methylmalonic acidemia and is attenuated by an engineered sirtuin
Head, P. E., Myung, S., Chen, Y., Schneller, J. L., Wang, C., Duncan, N., Hoffman, P., Chang, D., Gebremariam, A., Gucek, M., et al. (2022) · Science Translational Medicine · doi:10.1126/scitranslmed.abn4772 · Cited by 52
Small protein modules dictate prophage fates during polylysogeny
Silpe, J. E., Duddy, O. P., Johnson, G. E., Beggs, G. A., Hussain, F. A., Forsberg, K. J., & Bassler, B. L. (2023) · Nature · doi:10.1038/s41586-023-06376-y · Cited by 52
On the lifetime of bioinformatics web services
Kern, F., Fehlmann, T., & Keller, A. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa1125 · Cited by 50
Phylogenomics Identifies a New Major Subgroup of Apicomplexans, Marosporida class nov., with Extreme Apicoplast Genome Reduction
Mathur, V., Kwong, W. K., Husnik, F., Irwin, N. A. T., Kristmundsson, Á., Gestal, C., Freeman, M., & Keeling, P. J. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evaa244 · Cited by 50
A novel unsaturated β-glucuronyl hydrolase involved in ulvan degradation unveils the versatility of stereochemistry requirements in family GH105
Collén, P. N., Jeudy, A., Sassi, J.-F., Groisillier, A., Czjzek, M., Coutinho, P. M., & Helbert, W. (2014) · Journal of Biological Chemistry · doi:10.1074/jbc.m113.537480 · Cited by 47
Characterisation of lactic acid bacteria in spontaneously fermented camel milk and selection of strains for fermentation of camel milk.
Fugl, A., Berhe, T., Kiran, A., Hussain, S., Laursen, M. F., Bahl, M. I., Hailu, Y., Sørensen, K. I., Guya, M. E., Ipsen, R., et al. (2017) · International Dairy Journal · doi:10.1016/j.idairyj.2017.04.007 · Cited by 44
Regulation of RAS palmitoyltransferases by accessory proteins and palmitoylation
Yang, A., Liu, S., Zhang, Y., Chen, J., Fan, Y., Wang, F., Zou, Y., Feng, S., Wu, J., & Hu, Q. (2024) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-01183-5 · Cited by 38
Comparative mucomic analysis of three functionally distinct Cornu aspersum Secretions
Cerullo, A. R., McDermott, M. B., Pepi, L. E., Liu, Z.-L., Barry, D., Zhang, S., Yang, X., Chen, X., Azadi, P., Holford, M., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-41094-z · Cited by 35
Genomic and phenotypic evolution of nematode-infecting microsporidia
Wadi, L., El Jarkass, H. T., Tran, T. D., Islah, N., Luallen, R. J., & Reinke, A. W. (2023) · PLOS Pathogens · doi:10.1371/journal.ppat.1011510 · Cited by 32
Sarecycline inhibits protein translation in Cutibacterium acnes 70S ribosome using a two-site mechanism
Lomakin, I. B., Devarkar, S. C., Patel, S., Grada, A., & Bunick, C. G. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad103 · Cited by 25
Complete Genome Sequence of the Newly Developed Lactobacillus acidophilus Strain With Improved Thermal Adaptability
Jeon, S., Kim, H., Choi, Y., Cho, S., Seo, M., & Kim, H. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.697351 · Cited by 23
SSR identification and phylogenetic analysis in four plant species based on complete chloroplast genome sequences
Zhu, Y., Zhang, X., Yan, S., Feng, C., Wang, D., Yang, W., Daud, M. K., Xiang, J., & Mei, L. (2023) · Plasmid · doi:10.1016/j.plasmid.2023.102670 · Cited by 24
ERK2 MAP kinase regulates SUFU binding by multisite phosphorylation of GLI1
Bardwell, A. J., Wu, B., Sarin, K. Y., Waterman, M. L., Atwood, S. X., & Bardwell, L. (2022) · Life Science Alliance · doi:10.26508/lsa.202101353 · Cited by 20
Activation of ChvG-ChvI regulon by cell wall stress confers resistance to β-lactam antibiotics and initiates surface spreading in Agrobacterium tumefaciens
(2022) · doi:10.1371/journal.pgen.1010274 · Cited by 18
Frustraevo: a web server to localize and quantify the conservation of local energetic frustration in protein families
Parra, R. G., Freiberger, M. I., Poley-Gil, M., Fernandez-Martin, M., Radusky, L. G., Ruiz-Serra, V., Wolynes, P. G., Ferreiro, D. U., & Valencia, A. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae244 · Cited by 10
WIV, a protein domain found in a wide number of arthropod viruses, which probably facilitates infection
Karlin, D. G. (2024) · Journal of General Virology · doi:10.1099/jgv.0.001948 · Cited by 8
A genome-scale drug discovery pipeline uncovers therapeutic targets and a unique p97 allosteric binding site in Schistosoma mansoni
(2025) · doi:10.1073/pnas.2505710122 · Cited by 8
Burkholderia pseudomallei Complex Subunit and Glycoconjugate Vaccines and Their Potential to Elicit Cross-Protection to Burkholderia cepacia Complex
Badten, A. J., & Torres, A. G. (2024) · Vaccines · doi:10.3390/vaccines12030313 · Cited by 8
‘Microbial monitoring in the EDEN ISS greenhouse, a mobile test facility in antarctica’.
Fahrion, J., Fink, C., Zabel, P., Schubert, D., Mysara, M., Van Houdt, R., Eikmanns, B., Beblo-Vranesevic, K., & Rettberg, P. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.00525 · Cited by 7
Functional consequences of reductive protein evolution in a minimal eukaryotic genome
Jiang, J., Qu, R., Grigorescu, M., Zhao, W., Yu, Q. Y., Shreenidhi, P. M., Tamim El Jarkass, H., & Reinke, A. W. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.116333 · Cited by 7
A comprehensive review of global alignment of multiple biological networks: background, applications and open issues
Girisha, M. N., Badiger, V. P., & Pattar, S. (2022) · Network Modeling Analysis in Health Informatics and Bioinformatics · doi:10.1007/s13721-022-00353-7 · Cited by 4
Somatic Mutations in HLA Class Genes and Antigen-Presenting Molecules in Malignant Glioma
Schulte, S. C., Peter, W., Rosenberger, G., Schäfer, M., Maire, C. L., Rünger, A., Ryba, A., Riecken, K., Fita, K. D., Matschke, J., et al. (2025) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-24-0419 · Cited by 3
Flattening the curve—How to get better results with small deep‐mutational‐scanning datasets
Wirnsberger, G., Pritišanac, I., Oberdorfer, G., & Gruber, K. (2024) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26686 · Cited by 3
Screening of promising molecules against potential drug targets in Yersinia pestis by integrative pan and subtractive genomics, docking and simulation approach
(2024) · doi:10.1007/s00203-024-04140-y · Cited by 2
Identification and evaluation of tumor pyroptosis-associated antigens for design a vaccine candidate against lung cancer
(2026) · doi:10.1038/s41598-024-84792-4

Authors: Johnson, M., Zaretskaya, I., Raytselis, Y., Merezhuk, Y., McGinnis, S., & Madden, T. L.
Venue: Nucleic Acids Research
Publisher: Oxford University Press (OUP)
Published: 2008-05-19
Volume: 36
Issue: Web Server
Pages: W5-W9
ISSN: 0305-1048 (ISSN-L)
1362-4962
DOI: 10.1093/nar/gkn201
OpenAlex: W2146341019
Cited by: 4,232
References: 2
FWCI: 18.74
Type: journal article
Language: en
Open access: gold
Licence: creativecommons.org/licenses/by-nc/2.0/uk/ (vor, 3101 d)

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 ›

Are you an author, or do you see a problem with this page? Request a review

Data sources

Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.

NCBI BLAST: a better web interface

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Self-check

Citations

Cites

Cited by

Metadata

Record

About these checks

Data sources