BLAST: a more efficient report with usability improvements
Open accessAbstract
The Basic Local Alignment Search Tool (BLAST) website at the National Center for Biotechnology (NCBI) is an important resource for searching and aligning sequences. A new BLAST report allows faster loading of alignments, adds navigation aids, allows easy downloading of subject sequences and reports and has improved usability. Here, we describe these improvements to the BLAST report, discuss design decisions, describe other improvements to the search page and database documentation and outline plans for future development. The NCBI BLAST URL is http://blast.ncbi.nlm.nih.gov.
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The noncanonical MYBPC3 peptide had not been observed in PeptideAtlas or MassIVE-KB and had no identical match to any sequences of any taxonomy in RefSeq by BLASTP.
“The noncanonical peptide had not been observed in the peptide repositories PeptideAtlas (housing 1.4M peptides) (Deutsch et al., 2015) or MassIVE-KB (2.3 M peptides) (Wang et al., 2018a) and had no identical match to any sequences of any taxonomy in RefSeq by BLASTP (Boratyn et al., 2013).”
From Splice-Junction-Based Mapping of Alternative Isoforms in the Human Proteome (2019) · cites this paper as Boratyn et al., 2013
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Cites
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 · see citing works
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 · see citing works
Self-citationNCBI BLAST: a better web interface
Johnson, M., Zaretskaya, I., Raytselis, Y., Merezhuk, Y., McGinnis, S., & Madden, T. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn201 · Cited by 4,207 · see citing works
Self-citationBLAST: at the core of a powerful and diverse set of sequence analysis tools
McGinnis, S., & Madden, T. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh435 · Cited by 2,173 · see citing works
Self-citationSchäffer, A. A. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.14.2994 · Cited by 1,375 · see citing works
Database indexing for production MegaBLAST searches
Morgulis, A. O., Coulouris, G., Raytselis, Y., Madden, T., Agarwala, R., & Schäffer, A. A. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn322 · Cited by 1,352 · see citing works
Self-citationDomain enhanced lookup time accelerated BLAST
Boratyn, G. M., Schäffer, A. A., Agarwala, R., Altschul, S. F., Lipman, D. J., & Madden, T. (2012) · Biology Direct · doi:10.1186/1745-6150-7-12 · Cited by 795 · see citing works
Self-citationBLAST: improvements for better sequence analysis
Ye, J., McGinnis, S., & Madden, T. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl164 · Cited by 774 · see citing works
Self-citationZhang, J., & Madden, T. (1997) · Genome Research · doi:10.1101/gr.7.6.649 · Cited by 360 · see citing works
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Grigoriev, I. V., Nikitin, R., Haridas, S., Kuo, A., Ohm, R., Otillar, R., Riley, R., Salamov, A., Zhao, X., Korzeniewski, F., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1183 · Cited by 1,498 · see citing works
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Lau, E., Han, Y., Williams, D. R., Thomas, C. T., Shrestha, R., Wu, J. C., & Lam, M. P. Y. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.11.026 · Cited by 67 · see citing works
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Boström, A. E., Ciuculete, D.-M., Attwood, M., Krattinger, R., Nikontovic, L., Titova, O. E., Kullak-Ublick, G. A., Mwinyi, J., & Schiöth, H. B. (2017) · Journal of Affective Disorders · doi:10.1016/j.jad.2017.05.017 · Cited by 33 · see citing works
Boström, A. E., Chatzittofis, A., Ciuculete, D.-M., Flanagan, J. N., Krattinger, R., Bandstein, M., Mwinyi, J., Kullak-Ublick, G. A., Öberg, K. G., Arver, S., et al. (2020) · Epigenetics · doi:10.1080/15592294.2019.1656157 · Cited by 25 · see citing works
Function and evolution of two forms of SecDF homologs in Streptomyces coelicolor.
Zhou, Z., Li, Y., Sun, N., Sun, Z., Lv, L., Wang, Y., Shen, L., & Li, Y.-Q. (2014) · PLoS ONE · doi:10.1371/journal.pone.0105237 · Cited by 13 · see citing works
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- Authors
- 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., Raytselis, Y., Sayers, E. W., Tao, T., Ye, J., & Zaretskaya, I.
- Affiliations
- National Institutes of Health (US)
- Corresponding author
- Madden, Thomas L.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-04-22
- Volume
- 41
- Issue
- W1
- Pages
- W29-W33
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC3692093
- OpenAlex
- W2067964678
- Cited by
- 1,369
- References
- 9
- Citations by year
- 2026: 89 · 2025: 143 · 2024: 171 · 2023: 176 · 2022: 144 · 2021: 115 · 2020: 113 · 2019: 105 · 2018: 105 · 2017: 79 · 2016: 59 · 2015: 36 · 2014: 24 · 2013: 9 · 2012: 1
- FWCI
- 19.45
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nucleic Acids Research (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion, public-domain)
- PubMed Central (publishedVersion, public-domain)
- PubMed (publishedVersion)
- 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
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
- Keywords
- BLAST, sequence alignment, website usability, sequence database searching, database documentation, web design
- MeSH terms
- Animals, Software, Sequence Alignment, Internet, Genomics, L-Gulonolactone Oxidase, Rats
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