Alignment of whole genomes

Nucleic Acids Research

Volumn 27, Issue 11, 1999, Pages 2369-2376

  Delcher, Arthur L ^a,b   Kasif, Simon ^c   Fleischmann, Robert D ^d   Peterson, Jeremy ^d   White, Owen ^d   Salzberg, Steven L ^d  

^a LOYOLA UNIVERSITY MARYLAND   (United States)

^b CELERA GENOMICS   (United States)

^c University of Illinois at Chicago   (United States)

^d J CRAIG VENTER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE;

ALGORITHM; ARTICLE; CHROMOSOME 12; CHROMOSOME 6; COMPUTER ANALYSIS; DATA ANALYSIS; EVOLUTION; GENE DUPLICATION; GENE SEQUENCE; GENE TRANSLOCATION; GENOME; HUMAN; MOUSE; MYCOPLASMA; NONHUMAN; PRIORITY JOURNAL;

ALGORITHMS; ANIMALS; BASE SEQUENCE; DNA; GENOME, BACTERIAL; HUMANS; MICE; MOLECULAR SEQUENCE DATA; MYCOPLASMA; SEQUENCE ALIGNMENT;

MYCOPLASMA; MYCOPLASMA TUBERCULOSIS; PROKARYOTA;

EID: 0033153375     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/27.11.2369     Document Type: Article

References (32)

1. Fleischmann,R.D., Adams,M., White,O., Clayton,R., Kirkness,E., Kerlavage,A., Bult,C., Tomb,J.-F., Dougherty,B., Merrick,J., McKenney,K., Sutton,G., FitzHugh,W., Fields,C., Gocayne,J., Scott,J., Shirley,R., Liu,L.-I., Glodek,A., Kelley,J., Weidman,J., Phillips,C., Spriggs,T., Hedblom,E., Cotton,M., Utterback,T., Hanna,M., Nguyen,D., Saudek,D., Brandon,R., Fine,L., Fritchman,J., Fuhrmann,J., Geoghagen,N., Gnehm,C., McDonald,L., Small,K., Fraser,C., Smith,H. and Venter,J.C. (1995) Science, 269, 496-512.
2. Fraser,C.M., Gocayne,J., White,O., Adams,M., Clayton,R., Fleischmann,R., Bult,C., Kerlavage,A., Sutton,G., Kelley,J., Fritchman,J., Weidman,J., Small,K., Sandusky,M., Fuhrmann,J., Nguyen,D., Utterback,T., Saudek,R., Phillips,C., Merrick,J., Tomb,J.-F., Dougherty,B., Bott,K., Hu,R-C., Lucier,T., Peterson,S., Smith,H., Hutchison,C. and Venter,J.C. (1995) Science, 270, 397-403.
3. Himmelreich,R., Hilbert,H., Plagens,H., Pirkl,E., Li,B.C. and Herrmann,R. (1996) Nucleic Acids Res., 24, 4420-4449.
4. Cole,S.T., Brosch,R., Parkhill,J., Garnier,T., Churcher,C., Harris,D., Gordon,S.V., Eiglmeier,K., Gas,S., Barry,C.E., Tekaia,F., Badcock,K., Basham,D., Brown,D., Chillingworth,T., Connor,R., Davies,R., Devlin,K., Feltwell,T., Gentles,S., Hamlin,N., Holroyd,S., Hornsby,T., Jagels,K. and Barrell,B. (1998) Nature, 393, 537-544.
5. Stephens,R., Kalman,S., Lammel,C., Fan,J., Marathe,R., Aravind,L., Mitchell,W., Olinger,L., Tatusov,R., Zhao,Q., Koonin,E. and Davis,R. (1998) Science, 282, 754-759.
6. Needleman,S. and Wunsch,C. (1970) J. Mol. Biol., 48, 443-453.
7. Smith,T. and Waterman,M. (1981) J. Mol. Biol., 147, 195-197.
8. Pearson,W.R. (1995) Prot. Sci., 4, 1145-1160.
9. Gusfield,D. (1997) Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology. Cambridge University Press, New York.
10. Waterman,M. (1995) Introduction to Computational Biology: Maps, Sequences and Genomes. Chapman & Hall, New York.
11. Lipman,D.J. and Pearson,W.R. (1985) Science, 227, 1435-1441.
12. Benson,G. (1999) Nucleic Acids. Res., 27, 573-580.
13. Chao,K.-M., Zhang,J., Ostell,J. and Miller,W. (1997) Comput. Appl. Biosci., 13, 75-80.
14. Chao,K.-M., Zhang,J., Ostell,J. and Miller,W. (1995) Comput. Appl. Biosci., 11, 147-153.
15. Altschul,S., Gish,W., Miller,W., Myers,E. and Lipman,D. (1990) J. Mol. Biol., 215, 403-410.
16. Altschul,S., Madden,T., Schaffer,A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D. (1997) Nucleic Acids Res., 25, 3389-3402.
17. Weiner,P. (1973) Linear pattern matching algorithms. In Proc. 14th IEEE Symp. Switching & Automata Theory. pp. 1-11.
18. McCreight,E.M. (1976) J. ACM, 23, 262-272.
19. Brazma,A., Jonassen,I., Vilo,J. and Ukkonen,E. (1998) Genome Res., 8, 1202-1215.
20. Chen,M.T. and Seiferas,J. (1985) In Apostolico,A. and Galil,Z. (eds), Combinatorial Algorithms on Words. Springer-Verlag, New York, pp. 97-107.
21. Ukkonen,E. (1995) Algorithmica, 14, 249-260.
22. Kurtz,S. (1998) Reducing the space requirement of suffix trees. Technical Report 98-03, Universität at Bielefeld, Bielefeld, Germany.
23. Weiss,K.N. (1998) Genome Res., 8, 691-697.
24. Taillon-Miller,P., Gu,Z., Li,Q., Hillier,L. and Kwok,P.-Y. (1998) Genome Res., 8, 748-754.
25. Valway,S.E., Sanchez,M.P., Shinnick,T.F.,.Orme,I., Agerton,T., Hoy,D., Jones,J.S, Westmoreland,H. and Onorato,I.M. (1997) N. Engl. J. Med., 338, 633-639.
26. Sreevatsan.S., Pan,X., Stockbauer,K.E., Connell,N.D., Kreiswirth,B.N., Whittam,J.S. and Musser,J.M. (1997) Proc. Natl Acad. Sci. USA, 94, 9869-9874.
27. Himmelreich,R., Plagens,H., Hilbert,H., Reiner,B. and Herrmann,R. (1997) Nucleic Acids Res., 25, 701-712.
28. Ansari-Lari,M., Oeltjen,J.C., Schwartz,S., Zhang,Z., Muzny,D.M., Lu,J., Gorrell,J.H., Chinault,A.C., Belmont,J.W., Miller,W. and Gibbs,R.A. (1998) Genome Res., 8, 29-40.
29. Sonnhammer,E. and Durbin,R. (1995) Gene, 167, GC1-GC10.
30. Huang,X., Hardison,R. and Miller,W. (1990) Comput. Appl. Biosci., 6, 373-381.
31. Schwartz,S., Miller,W., Yang,C.-M. and Hardison R.C. (1991) Nucleic Acids Res., 19, 4663-4667.
32. Oeltjen,J.C., Malley,T.M., Muzny,D.M., Miller,W., Gibbs,R.A. and Belmont,J.W. (1997) Genome Res., 7, 315-329.