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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Altschul SF, et al. Nucleic Acids Res. 1997 Sep 1;25(17):3389-402. doi: 10.1093/nar/25.17.3389. Nucleic Acids Res. 1997. PMID: 9254694 Free PMC article. Review.
Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Altschul SF, et al. J Mol Biol. 1990 Oct 5;215(3):403-10. doi: 10.1016/S0022-2836(05)80360-2. J Mol Biol. 1990. PMID: 2231712
Dynamic programming algorithms for biological sequence comparison.
Pearson WR, Miller W. Pearson WR, et al. Methods Enzymol. 1992;210:575-601. doi: 10.1016/0076-6879(92)10029-d. Methods Enzymol. 1992. PMID: 1584052
A tool for aligning very similar DNA sequences.
Chao KM, Zhang J, Ostell J, Miller W. Chao KM, et al. Comput Appl Biosci. 1997 Feb;13(1):75-80. doi: 10.1093/bioinformatics/13.1.75. Comput Appl Biosci. 1997. PMID: 9088712
Alignment of Escherichia coli K12 DNA sequences to a genomic restriction map.
Rudd KE, Miller W, Ostell J, Benson DA. Rudd KE, et al. Nucleic Acids Res. 1990 Jan 25;18(2):313-21. doi: 10.1093/nar/18.2.313. Nucleic Acids Res. 1990. PMID: 2183179 Free PMC article.
Mapping sequenced E.coli genes by computer: software, strategies and examples.
Rudd KE, Miller W, Werner C, Ostell J, Tolstoshev C, Satterfield SG. Rudd KE, et al. Nucleic Acids Res. 1991 Feb 11;19(3):637-47. doi: 10.1093/nar/19.3.637. Nucleic Acids Res. 1991. PMID: 2011534 Free PMC article.
Software tools for analyzing pairwise alignments of long sequences.
Schwartz S, Miller W, Yang CM, Hardison RC. Schwartz S, et al. Nucleic Acids Res. 1991 Sep 11;19(17):4663-7. doi: 10.1093/nar/19.17.4663. Nucleic Acids Res. 1991. PMID: 1891357 Free PMC article.
Web-based visualization tools for bacterial genome alignments.
Florea L, Riemer C, Schwartz S, Zhang Z, Stojanovic N, Miller W, McClelland M. Florea L, et al. Nucleic Acids Res. 2000 Sep 15;28(18):3486-96. doi: 10.1093/nar/28.18.3486. Nucleic Acids Res. 2000. PMID: 10982867 Free PMC article.
Winnowing sequences from a database search.
Berman P, Zhang Z, Wolf YI, Koonin EV, Miller W. Berman P, et al. J Comput Biol. 2000 Feb-Apr;7(1-2):293-302. doi: 10.1089/10665270050081531. J Comput Biol. 2000. PMID: 10890403
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