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Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements
Open accessAbstract
PSI-BLAST is an iterative program to search a database for proteins with distant similarity to a query sequence. We investigated over a dozen modifications to the methods used in PSI-BLAST, with the goal of improving accuracy in finding true positive matches. To evaluate performance we used a set of 103 queries for which the true positives in yeast had been annotated by human experts, and a popular measure of retrieval accuracy (ROC) that can be normalized to take on values between 0 (worst) and 1 (best). The modifications we consider novel improve the ROC score from 0.758 +/- 0.005 to 0.895 +/- 0.003. This does not include the benefits from four modifications we included in the 'baseline' version, even though they were not implemented in PSI-BLAST version 2.0. The improvement in accuracy was confirmed on a small second test set. This test involved analyzing three protein families with curated lists of true positives from the non-redundant protein database. The modification that accounts for the majority of the improvement is the use, for each database sequence, of a position-specific scoring system tuned to that sequence's amino acid composition. The use of composition-based statistics is particularly beneficial for large-scale automated applications of PSI-BLAST.
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Cites
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
Cited by
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662
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
Accelerated Profile HMM Searches
Eddy, S. R. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002195 · Cited by 6,975
FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix
Price, M. N., Dehal, P. S., & Arkin, A. P. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp077 · Cited by 5,602
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
Human CtIP promotes DNA end resection
Sartori, A. A., Lukas, C., Coates, J., Mistrik, M., Fu, S., Bartek, J., Baer, R., Lukas, J., & Jackson, S. P. (2007) · Nature · doi:10.1038/nature06337 · Cited by 1,362
Some remarks on protein attribute prediction and pseudo amino acid composition
Chou, K.-C. (2011) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2010.12.024 · Cited by 1,225
Database Resources of the National Center for Biotechnology Information
Coordinators, N. R. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw1071 · Cited by 817
Database resources of the National Center for Biotechnology Information
Wheeler, D. L., Barrett, T., Benson, D. A., Bryant, S. H., Canese, K., Chetvernin, V., Church, D. M., DiCuccio, M., Edgar, R., Federhen, S., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkl1031 · Cited by 734
Comparative genomics and evolution of proteins involved in RNA metabolism
Anantharaman, V. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.7.1427 · Cited by 541
RAG1 Core and V(D)J Recombination Signal Sequences Were Derived from Transib Transposons
Kapitonov, V. V., & Jurka, J. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030181 · Cited by 521
Protein structure determination using metagenome sequence data
Ovchinnikov, S., Park, H., Varghese, N., Huang, P.-S., Pavlopoulos, G. A., Kim, D. E., Kamisetty, H., Kyrpides, N. C., & Baker, D. (2017) · Science · doi:10.1126/science.aah4043 · Cited by 520
Anantharaman, V., & Aravind, L. (2003) · Genome Biology · doi:10.1186/gb-2003-4-2-r11 · Cited by 365
Thompson, J. D., Linard, B., Lecompte, O., & Poch, O. (2011) · PLoS ONE · doi:10.1371/journal.pone.0018093 · Cited by 242
Protein sequence design with a learned potential
Anand, N., Eguchi, R., Mathews, I. I., Perez, C. P., Derry, A., Altman, R. B., & Huang, P.-S. (2022) · Nature Communications · doi:10.1038/s41467-022-28313-9 · Cited by 171
TRAM, LAG1 and CLN8: members of a novel family of lipid-sensing domains?
Winter, E., & Ponting, C. P. (2002) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(02)02154-0 · Cited by 181
Bandyopadhyay, A., Elvitigala, T., Welsh, E., Stöckel, J., Liberton, M., Min, H., Sherman, L. A., & Pakrasi, H. B. (2011) · mBio · doi:10.1128/mbio.00214-11 · Cited by 102
Promponas, V. J., Iliopoulos, I., & Ouzounis, C. A. (2015) · Standards in Genomic Sciences · doi:10.1186/s40793-015-0101-2 · Cited by 43
Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor
Appler, K. E., Lingford, J. P., Gong, X., Panagiotou, K., Leão, P., Langwig, M. V., Greening, C., Ettema, T. J. G., De Anda, V., & Baker, B. J. (2026) · Nature · doi:10.1038/s41586-026-10128-z · Cited by 36
Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor
Appler, K. E., Lingford, J. P., Gong, X., Panagiotou, K., Leão, P., Langwig, M., Greening, C., Ettema, T. J. G., De Anda, V., & Baker, B. J. (2024) · doi:10.1101/2024.07.04.601786 · Cited by 36
Lv, X., Chen, J., Lu, Y., Chen, Z., Xiao, N., & Yang, Y. (2020) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.0c00064 · Cited by 26
PRESCOTT: a population aware, epistatic, and structural model accurately predicts missense effects
Tekpinar, M., David, L., Henry, T., & Carbone, A. (2025) · Genome Biology · doi:10.1186/s13059-025-03581-y · Cited by 18
Zile, K., Dessimoz, C., Wurm, Y., & Masel, J. (2020) · Genome Biology and Evolution · doi:10.1093/gbe/evaa127 · Cited by 18
Metadata
- Authors
- Schaffer, A. A.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2001-07-15
- Volume
- 29
- Issue
- 14
- Pages
- 2994-3005
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2133312664
- Cited by
- 1,386
- References
- 2
- FWCI
- 17.59
- Type
- journal article
- Language
- en
- Open access
- bronze
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