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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.
The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.
Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, Searle S, Farrell CM, Loveland JE, Ruef BJ, Hart E, Suner MM, Landrum MJ, Aken B, Ayling S, Baertsch R, Fernandez-Banet J, Cherry JL, Curwen V, Dicuccio M, Kellis M, Lee J, Lin MF, Schuster M, Shkeda A, Amid C, Brown G, Dukhanina O, Frankish A, Hart J, Maidak BL, Mudge J, Murphy MR, Murphy T, Rajan J, Rajput B, Riddick LD, Snow C, Steward C, Webb D, Weber JA, Wilming L, Wu W, Birney E, Haussler D, Hubbard T, Ostell J, Durbin R, Lipman D. Pruitt KD, et al. Genome Res. 2009 Jul;19(7):1316-23. doi: 10.1101/gr.080531.108. Epub 2009 Jun 4. Genome Res. 2009. PMID: 19498102 Free PMC article.
Splign: algorithms for computing spliced alignments with identification of paralogs.
Kapustin Y, Souvorov A, Tatusova T, Lipman D. Kapustin Y, et al. Biol Direct. 2008 May 21;3:20. doi: 10.1186/1745-6150-3-20. Biol Direct. 2008. PMID: 18495041 Free PMC article.
Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signals.
Shabalina SA, Ogurtsov AY, Rogozin IB, Koonin EV, Lipman DJ. Shabalina SA, et al. Nucleic Acids Res. 2004 Mar 18;32(5):1774-82. doi: 10.1093/nar/gkh313. Print 2004. Nucleic Acids Res. 2004. PMID: 15031317 Free PMC article.
The relationship of protein conservation and sequence length.
Lipman DJ, Souvorov A, Koonin EV, Panchenko AR, Tatusova TA. Lipman DJ, et al. BMC Evol Biol. 2002 Nov 1;2:20. doi: 10.1186/1471-2148-2-20. Epub 2002 Nov 1. BMC Evol Biol. 2002. PMID: 12410938 Free PMC article.
GenBank.
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL. Benson DA, et al. Nucleic Acids Res. 2002 Jan 1;30(1):17-20. doi: 10.1093/nar/30.1.17. Nucleic Acids Res. 2002. PMID: 11752243 Free PMC article.
CDART: protein homology by domain architecture.
Geer LY, Domrachev M, Lipman DJ, Bryant SH. Geer LY, et al. Genome Res. 2002 Oct;12(10):1619-23. doi: 10.1101/gr.278202. Genome Res. 2002. PMID: 12368255 Free PMC article.
GenBank.
Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. Benson DA, et al. Among authors: lipman dj. Nucleic Acids Res. 2017 Jan 4;45(D1):D37-D42. doi: 10.1093/nar/gkw1070. Epub 2016 Nov 28. Nucleic Acids Res. 2017. PMID: 27899564 Free PMC article.
GenBank.
Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. Clark K, et al. Among authors: lipman dj. Nucleic Acids Res. 2016 Jan 4;44(D1):D67-72. doi: 10.1093/nar/gkv1276. Epub 2015 Nov 20. Nucleic Acids Res. 2016. PMID: 26590407 Free PMC article.
GenBank.
Benson DA, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. Benson DA, et al. Among authors: lipman dj. Nucleic Acids Res. 2015 Jan;43(Database issue):D30-5. doi: 10.1093/nar/gku1216. Epub 2014 Nov 20. Nucleic Acids Res. 2015. PMID: 25414350 Free PMC article.
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