The DOI matches its Crossref record; 84 of the 94 references it cites were found in a registry or an index.
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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“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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Citations
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
Self-citationFischler, M. A., & Bolles, R. C. (1981) · Communications of the ACM · doi:10.1145/358669.358692 · Cited by 25,893
Needleman, S. B., & Wunsch, C. D. (1970) · Journal of Molecular Biology · doi:10.1016/0022-2836(70)90057-4 · Cited by 11,288
Improved tools for biological sequence comparison.
Pearson, W. R., & Lipman, D. J. (1988) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.85.8.2444 · Cited by 11,227
Identification of common molecular subsequences
Smith, T. F., & Waterman, M. S. (1981) · Journal of Molecular Biology · doi:10.1016/0022-2836(81)90087-5 · Cited by 9,962
Amino acid substitution matrices from protein blocks.
Henikoff, S., & Henikoff, J. G. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.22.10915 · Cited by 6,218
A Strong Candidate for the Breast and Ovarian Cancer Susceptibility Gene BRCA1
Miki, Y., Swensen, J. J., Shattuck-Eidens, D. M., Futreal, P. A., Harshman, K., Tavtigian, S. V., Liu, Q., Cochran, C., Bennett, L. M., Ding, W., et al. (1994) · Science · doi:10.1126/science.7545954 · Cited by 6,069
Atlas of protein sequence and structure
Chang, M.-Y., Dayhoff, M. O., Eck, R. V., & Sochard, M. R. (1965) · NASA Technical Reports Server (NASA) · Cited by 4,383
Least-Squares Fitting of Two 3-D Point Sets
Arun, K. S., Huang, T. S., & Blostein, S. D. (1987) · IEEE Transactions on Pattern Analysis and Machine Intelligence · doi:10.1109/tpami.1987.4767965 · Cited by 3,952
The SWISS-PROT protein sequence data bank and its supplement TrEMBL
Bairoch, A., & Apweiler, R. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.1.31 · Cited by 3,594
Research works printed but not linked: 16
- [2]2. Pearson,W.R. and Lipman,D.J. (1988) Proc. Natl. Acad. Sci. USA, 85, 2444-2448.
- [4]4. Chao,K.-M., Pearson,W.R. and Miller,W. (1992) Comput. Appl. Biosci., 8, 481-487.
- [8]8. Karlin,S. and Altschul,S.F. (1990) Proc. Natl. Acad. Sci. USA, 87, 2264-2268.
- [18]18. Henikoff,S. and Henikoff,J.G. (1992) Proc. Natl. Acad. Sci. USA, 89, 10915-10919.
- [19]19. Wilbur,W.J. and Lipman,D.J. (1983) Proc. Natl. Acad. Sci. USA, 80, 726-730.
- [20]20. Robinson,A.B. and Robinson,L.R. (1991) Proc. Natl. Acad. Sci. USA, 88, 8880-8884.
- [21]21. Karlin,S. and Altschul,S.F. (1993) Proc. Natl. Acad. Sci. USA, 90, 5873-5877.
- [28]28. McLachlan,A.D. (1983) J. Mol. Biol., 169, 15-30. Downloaded from https://academic.oup.com/nar/article/25/17/3389/1061651 by guest on 24 June 2023 29
- [34]34. Gribskov,M., McLachlan,A.D. and Eisenberg,D. (1987) Proc. Natl. Acad. Sci. USA, 84, 4355-4358.
- [36]36. Stormo,G.D. and Hartzell,G.W. III (1989) Proc. Natl. Acad. Sci. USA, 86, 1183-1187.
- [37]37. Tatusov,R.L., Altschul,S.F. and Koonin,E.V. (1994) Proc. Natl. Acad. Sci. USA, 91, 12091-12095.
- [53]53. Brown,M., Hughey,R., Krogh,A., Mian,I.S., Sjölander,K. and Haussler,D. (1993) In Hunter,L., Searls,D. and Shavlik,J. (eds.), Proceedings of the First International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 47-55.
- [55]55. Karplus,K. (1995) In Rawlings,C., Clark,D., Altman,R., Hunter,L., Lengauer,T. and Wodak,S. (eds.), Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 188-196.
- [83]83. Fitch,W.M. and Smith,T.F. (1983) Proc. Natl. Acad. Sci. USA, 80, 1382-1386.
- [86]86. Altschul,S.F. Proteins, in press. 87
- [90]90. Fulton,L. and Waterston,R. (1995) GenBank accession no. 1176713. Downloaded from https://academic.oup.com/nar/article/25/17/3389/1061651 by guest on 24 June 2023
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Fugmann, S. D., Messier, C., Novack, L. A., Cameron, R. A., & Rast, J. P. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0509720103 · Cited by 177
Deep conservation of the enhancer regulatory code in animals
Wong, E. S., Zheng, D., Tan, S. Z., Bower, N. I., Garside, V., Vanwalleghem, G., Gaiti, F., Scott, E., Hogan, B. M., Kikuchi, K., et al. (2020) · Science · doi:10.1126/science.aax8137 · Cited by 176
Influence of metabolic network structure and function on enzyme evolution
Vitkup, D., Kharchenko, P., & Wagner, A. (2006) · Genome biology · doi:10.1186/gb-2006-7-5-r39 · Cited by 175
Geomicrobiology of pyrite (FeS2) dissolution: Case study at Iron Mountain, California
Katrina J. Edwards, B. M. G. (1999) · Geomicrobiology Journal · doi:10.1080/014904599270668 · Cited by 175
Opsins and clusters of sensory G-protein-coupled receptors in the sea urchin genome
Raible, F., Tessmar-Raible, K., Arboleda, E., Kaller, T., Bork, P., Arendt, D., & Arnone, M. I. (2006) · Developmental Biology · doi:10.1016/j.ydbio.2006.08.070 · Cited by 170
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Lyra, A., Rinttilä, T., Nikkilä, J., Krogius-Kurikka, L., Kajander, K., Malinen, E., Mättö, J., Mäkelä, L., & Palva, A. (2009) · World Journal of Gastroenterology · doi:10.3748/wjg.15.5936 · Cited by 160
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Mulkidjanian, A. Y., Galperin, M. Y., Makarova, K. S., Wolf, Y. I., & Koonin, E. V. (2008) · Biology Direct · doi:10.1186/1745-6150-3-13 · Cited by 163
Simoni, E., Daniele, S., Bottegoni, G., Pizzirani, D., Trincavelli, M. L., Goldoni, L., Tarozzo, G., Reggiani, A., Martini, C., Piomelli, D., et al. (2012) · Journal of Medicinal Chemistry · doi:10.1021/jm3009458 · Cited by 163
Zanirati, D. F., Abatemarco, M., Sandes, S. H. D. C., Nicoli, J. R., Nunes, Á. C., & Neumann, E. (2015) · Anaerobe · doi:10.1016/j.anaerobe.2014.12.007 · Cited by 162
Romanowski, M. J., Soccio, R. E., Breslow, J. L., & Burley, S. K. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.052140699 · Cited by 162
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Aravind, L., Anantharaman, V., & Koonin, E. V. (2002) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10064 · Cited by 153
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Anghel, S. A., McGilvray, P. T., Hegde, R. S., & Keenan, R. J. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.12.006 · Cited by 150
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Nailis, H., Kucharíková, S., Řičicová, M., Van Dijck, P., Deforce, D., Nelis, H., & Coenye, T. (2010) · BMC Microbiology · doi:10.1186/1471-2180-10-114 · Cited by 157
Thompson, J. M., Jones, H. A., & Perry, R. D. (1999) · Infection and Immunity · doi:10.1128/iai.67.8.3879-3892.1999 · Cited by 154
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Wells, J. E., & Hylemon, P. B. (2000) · Applied and Environmental Microbiology · doi:10.1128/aem.66.3.1107-1113.2000 · Cited by 154
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YidC/Oxa1p/Alb3: evolutionarily conserved mediators of membrane protein assembly.
Luirink, J., Samuelsson, T., & de Gier, J.-W. (2001) · FEBS Letters · doi:10.1016/s0014-5793(01)02616-3 · Cited by 146
Lopez-Siles, M., Martinez-Medina, M., Surís-Valls, R., Aldeguer, X., Sabat-Mir, M., Duncan, S. H., Flint, H. J., & Garcia-Gil, L. J. (2016) · Inflammatory Bowel Diseases · doi:10.1097/mib.0000000000000590 · Cited by 144
Multi-domain, cell-envelope proteinases of lactic acid bacteria.
Siezen, R. J. (1999) · Antonie van Leeuwenhoek · doi:10.1023/a:1002036906922 · Cited by 144
Exo84 and Sec5 are competitive regulatory Sec6/8 effectors to the RalA GTPase
Jin, R., Junutula, J. R., Matern, H. T., Ervin, K. E., Scheller, R. H., & Brunger, A. T. (2005) · The EMBO Journal · doi:10.1038/sj.emboj.7600699 · Cited by 145
Light-driven anaerobic microbial oxidation of manganese
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Izumo is part of a multiprotein family whose members form large complexes on mammalian sperm
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Sorroche, F. G., Spesia, M. B., Zorreguieta, Á., & Giordano, W. (2012) · Applied and Environmental Microbiology · doi:10.1128/aem.07826-11 · Cited by 139
Frataxin interacts functionally with mitochondrial electron transport chain proteins
González-Cabo, P., Vázquez-Manrique, R. P., García-Gimeno, M. A., Sanz, P., & Palau, F. (2005) · Human Molecular Genetics · doi:10.1093/hmg/ddi214 · Cited by 140
Wiame, E., Delpierre, G., Collard, F., & Van Schaftingen, E. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m200863200 · Cited by 140
Xiong, P., Zhang, C., Zheng, W., & Zhang, Y. (2017) · Journal of Molecular Biology · doi:10.1016/j.jmb.2016.11.022 · Cited by 140
“Since the number of collected sequences is often much lower than that required for stable Boltzmann statistics, here it is necessary to make corrections to the amino acid probability in the interface multiple structural alignment (iMSA) according to amino acid substitutionmatrix [12].”
Gao, M., & Skolnick, J. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1012820107 · Cited by 139
Viral AlkB proteins repair RNA damage by oxidative demethylation
van den Born, E., Omelchenko, M. V., Bekkelund, A., Leihne, V., Koonin, E. V., Dolja, V. V., & Falnes, P. Ø. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn519 · Cited by 134
“The set of viral, bacterial and eukaryotic AlkB proteins for phylogenetic analysis was identified using PSI-BLAST searches (22) against the nonredundant database of protein sequences (NCBI, NIH).”
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Bioinformatics curriculum guidelines: Toward a definition of core competencies
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Arboleya, S., Ruas-Madiedo, P., Margolles, A., Solís, G., Salminen, S., de los Reyes-Gavilán, C. G., & Gueimonde, M. (2011) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2010.10.036 · Cited by 139
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Bobrowicz, P., Pawlak, R., Correa, A., Bell‐Pedersen, D., & Ebbole, D. J. (2002) · Molecular Microbiology · doi:10.1046/j.1365-2958.2002.03052.x · Cited by 132
Zhang, X., Kurnasov, O. V., Karthikeyan, S., Grishin, N. V., Osterman, A. L., & Zhang, H. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m300073200 · Cited by 136
Procko, E., Berguig, G. Y., Shen, B. W., Song, Y., Frayo, S., Convertine, A. J., Margineantu, D., Booth, G., Correia, B. E., Cheng, Y., et al. (2014) · Cell · doi:10.1016/j.cell.2014.04.034 · Cited by 127
Bertea, C. M., Voster, A., Verstappen, F. W. A., Maffei, M., Beekwilder, J., & Bouwmeester, H. J. (2006) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2006.02.026 · Cited by 134
Kunik, V., Ashkenazi, S., & Ofran, Y. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks480 · Cited by 132
Genome-Wide Survey and Developmental Expression Mapping of Zebrafish SET Domain-Containing Genes
Sun, X.-J., Xu, P.-F., Zhou, T., Hu, M., Fu, C.-T., Zhang, Y., Jin, Y., Chen, Y., Chen, S.-J., Huang, Q.-H., et al. (2008) · PLoS ONE · doi:10.1371/journal.pone.0001499 · Cited by 127
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Dunin-Horkawicz, S., Feder, M., & Bujnicki, J. M. (2006) · BMC Genomics · doi:10.1186/1471-2164-7-98 · Cited by 133
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Pu, L., Govindaraj, R. G., Lemoine, J. M., Wu, H.-C., & Brylinski, M. (2019) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1006718 · Cited by 133
Light attention predicts protein location from the language of life
Stärk, H., Dallago, C., Heinzinger, M., & Rost, B. (2021) · Bioinformatics Advances · doi:10.1093/bioadv/vbab035 · Cited by 130
Frank, M. G., Weber, M. D., Fonken, L. K., Hershman, S. A., Watkins, L. R., & Maier, S. F. (2016) · Brain, Behavior, and Immunity · doi:10.1016/j.bbi.2015.10.009 · Cited by 133
Coordinating Bacterial Cell Division with Nutrient Availability: a Role for Glycolysis
Monahan, L. G., Hajduk, I. V., Blaber, S. P., Charles, I. G., & Harry, E. J. (2014) · mBio · doi:10.1128/mbio.00935-14 · Cited by 123
T Cell Responses to Human Endogenous Retroviruses in HIV-1 Infection
Garrison, K. E., Jones, R. B., Meiklejohn, D. A., Anwar, N., Ndhlovu, L. C., Chapman, J. M., Erickson, A. L., Agrawal, A., Spotts, G., Hecht, F. M., et al. (2007) · PLoS Pathogens · doi:10.1371/journal.ppat.0030165 · Cited by 131
A novel DNA modification by sulphur
Zhou, X., He, X., Liang, J., Li, A., Xu, T., Kieser, T., Helmann, J. D., & Deng, Z. (2005) · Molecular Microbiology · doi:10.1111/j.1365-2958.2005.04764.x · Cited by 131
Callebaut, I., Malivert, L., Fischer, A., Mornon, J.-P., Revy, P., & de Villartay, J.-P. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.c500473200 · Cited by 130
Prasai, T. P., Walsh, K. B., Bhattarai, S. P., Midmore, D. J., Van, T. T. H., Moore, R. J., & Stanley, D. (2016) · PLOS ONE · doi:10.1371/journal.pone.0154061 · Cited by 129
Walia, R. R., Xue, L. C., Wilkins, K., El-Manzalawy, Y., Dobbs, D., & Honavar, V. (2014) · PLoS ONE · doi:10.1371/journal.pone.0097725 · Cited by 132
“The PSSMs were constructed by running PSI-BLAST [61] against the NCBI nr database for three iterations with an E-value cutoff of 0.001 for inclusion in the next iteration.”
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Sherman, D. J., Martin, T., Nikolski, M., Cayla, C., Souciet, J.-L., & Durrens, P. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn859 · Cited by 129
Schnoes, A. M., Ream, D. C., Thorman, A. W., Babbitt, P. C., & Friedberg, I. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003063 · Cited by 129
Fujisawa, T., Narikawa, R., Okamoto, S., Ehira, S., Yoshimura, H., Suzuki, I., Masuda, T., Mochimaru, M., Takaichi, S., Awai, K., et al. (2010) · DNA Research · doi:10.1093/dnares/dsq004 · Cited by 128
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Hall, R. A., Bates, S., Lenardon, M. D., MacCallum, D. M., Wagener, J., Lowman, D. W., Kruppa, M. D., Williams, D. L., Odds, F. C., Brown, A. J. P., et al. (2013) · PLoS Pathogens · doi:10.1371/journal.ppat.1003276 · Cited by 128
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Garg, A., O’Rourke, J., Long, C., Doering, J., Ravenscroft, G., Bezprozvannaya, S., Nelson, B. R., Beetz, N., Li, L., Chen, S., et al. (2014) · Journal of Clinical Investigation · doi:10.1172/jci74994 · Cited by 127
Iwanaga, M., Toma, C., Miyazato, T., Insisiengmay, S., Nakasone, N., & Ehara, M. (2004) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.48.7.2364-2369.2004 · Cited by 126
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Muñoz-Gómez, S. A., Susko, E., Williamson, K., Eme, L., Slamovits, C. H., Moreira, D., López-García, P., & Roger, A. J. (2022) · Nature Ecology & Evolution · doi:10.1038/s41559-021-01638-2 · Cited by 111
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Kosloff, M., & Kolodny, R. (2008) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.21770 · Cited by 124
Roosens, N. H., Leplae, R., Bernard, C., & Verbruggen, N. (2005) · Planta · doi:10.1007/s00425-005-0006-1 · Cited by 113
Hull, C. M., Davidson, R. C., & Heitman, J. (2002) · Genes & Development · doi:10.1101/gad.1041402 · Cited by 119
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Wildman, D. E., Jameson, N. M., Opazo, J. C., & Yi, S. V. (2009) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2009.07.019 · Cited by 122
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Barrett, E., Kerr, C., Murphy, K., O'Sullivan, O., Ryan, C. A., Dempsey, E. M., Murphy, B. P., O'Toole, P. W., Cotter, P. D., Fitzgerald, G. F., et al. (2013) · Archives of Disease in Childhood - Fetal and Neonatal Edition · doi:10.1136/archdischild-2012-303035 · Cited by 120
Wu, D.-D., Irwin, D. M., & Zhang, Y.-P. (2008) · BMC Evolutionary Biology · doi:10.1186/1471-2148-8-241 · Cited by 121
Cohen, R., Elhadad, M., & Elhadad, N. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-10 · Cited by 121
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Fagnani, M., Barash, Y., Ip, J. Y., Misquitta, C., Pan, Q., Saltzman, A. L., Shai, O., Lee, L., Rozenhek, A., Mohammad, N., et al. (2007) · Genome Biology · doi:10.1186/gb-2007-8-6-r108 · Cited by 120
Arthur, J. C., Gharaibeh, R. Z., Uronis, J. M., Perez-Chanona, E., Sha, W., Tomkovich, S., Mühlbauer, M., Fodor, A. A., & Jobin, C. (2013) · Scientific Reports · doi:10.1038/srep02868 · Cited by 118
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Nakjang, S., Ndeh, D. A., Wipat, A., Bolam, D. N., & Hirt, R. P. (2012) · PLoS ONE · doi:10.1371/journal.pone.0030287 · Cited by 116
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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