Drosophila genomic sequence annotation using the BLOCKS+ database

Genome Research

Volumn 10, Issue 4, 2000, Pages 543-546

  Henikoff, Jorja G ^a   Henikoff, Steven ^a,b  

^a Fred Hutchinson Cancer Research Center   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; AUTOMATION; BASE PAIRING; CONTROLLED STUDY; DATA BASE; DROSOPHILA MELANOGASTER; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC CONSERVATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN FAMILY; SEQUENCE HOMOLOGY;

ALCOHOL DEHYDROGENASE; ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; DROSOPHILA MELANOGASTER; GENES, INSECT; GENOME; SEQUENCE HOMOLOGY, NUCLEIC ACID; SOFTWARE;

ARACHNIDA; DROSOPHILA MELANOGASTER; HEXAPODA; MELANOGASTER;

EID: 0034075809     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.10.4.543     Document Type: Article

References (22)

1. Adams, M.D., J.M. Kelley, J.D. Gocayne, M. Dubnick, M.H. Polymeropoulos, H. Xiao, C.R. Merril, A. Wu, B. Olde, R.F. Moreno, A.R. Kerlavage, W.R. McCombie, and J.C. Venter. 1991. Complementary DNA sequencing: Expressed sequence tags and human genome project. Science 252: 1651-1656.
2. Altschul, S.F., W. Gish, W. Miller, E.W. Myers, and D.J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
3. Ashburner, M., S. Misra, J. Roote, S.E. Lewis, R. Blazej, T. Davis, C. Doyle, R. Galle, R. George, N. Harris, G. Hartzell, D. Harvey, L. Hong, and K. Houston. 1999. An exploration of the sequence of a 2.9-Mb region of the genome of Drosophila melanogaster: the Adh region. Genetics 153: 179-219.
4. Attwood, T.K., D.R. Flower, A.P. Lewis, J.E. Mabey, S.R. Morgan, P. Scordis, J.N. Selley, and W. Wright. 1999. PRINTS prepares for the new millenium. Nucleic Acids Res. 27: 220-225.
5. Bateman, A., E. Birney, R. Durbin, S.R. Eddy, R.D. Finn, and E.L.L. Sonnhammer. 1999. Pram 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins. Nucleic Acids Res. 27: 260-262.
6. Birney, E. and R. Durbin. 2000. Using GeneWise in the Drosophila annotation experiment. Genome Res. (this issue).
7. Corpet, F., J. Gouzy, and D. Kahn. 1999. Recent improvements of the ProDom database of protein domain families. Nucleic Acids Res. 27: 263-267.
8. Fields, C.A. and C.A. Soderlund. 1990. gm: A practical tool for automating DNA sequence analysis. Comp. Appl. Biosci. 6: 263-270.
9. Gracy, J. and P. Argos. 1998. Automated protein sequence database classification. I. Integration of compositional similarity search, local similarity search, and multiple sequence alignment. Bioinformatics 14: 164-173.
10. Henikoff, J.G., E.A. Greene, S. Pietrokovski, and S. Henikoff. 2000. Increased coverage of protein families with the Blocks Database servers. Nucleic Acids Res. 28: 228-230.
11. Henikoff, S. and J.G. Henikoff. 1991. Automated assembly of protein blocks for database searching. Nucleic Acids Res. 19: 6565-6572.
12. _. 1994. A protein family classification method for analysis of large DNA sequences. In Proceedings of the 27th Annual Hawaii International Conference on Systems Sciences, pp. 265-274. Institute of Electrical and Electronics Engineers, New York, NY.
13. Henikoff, S. and J.C. Wallace. 1988. Detection of protein similarities using nucleotide sequence databases. Nucleic Acids Res. 16: 6191-6204.
14. Henikoff, S., J.G. Henikoff, W.J. Alford, and S. Pietrokovski. 1995. Automated construction and graphical presentation of protein blocks from unaligned sequences. Gene 163: GC17-GC26.
15. Henikoff, S., J.G. Henikoff, and S. Pietrokovski. 1999. Blocks+: A non-redundant database of protein alignment blocks derived from multiple compilations. Bioinformatics 15: 471-479.
16. Hofmann, K., P. Bucher, L. Falquet, and A. Bairoch. 1999. The PROSITE database, its status in 1999. Nucleic Acids Res. 27: 215-219.
17. Oliver, S.G., Q.J.M. van der Aart, M.L. Agostoni-Carbone, M. Aigle, L. Alberghina, D. Alexandraki, G. Antoine, R. Anwar, and J.P.G. Ballesta. 1992. The complete DNA sequence of yeast chromosome III. Nature 357: 38-46.
18. Pearson, W.R. and D.J. Lipman. 1988. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. 85: 2444-2448.
19. Pietrokovski, S. 1996. Searching databases of conserved sequence regions by aligning protein multiple-alignments. Nucleic Acids Res. 24: 3836-3845.
20. Reese, M.G., N. Harris, G. Hartzell, U. Ohler, and S. Lewis. 2000a. Genome annotation assessment in Drosophila melanogaster. Genome Res. (this issue).
21. Reese, M.G., D. Kulp, H. Tammana, and D. Haussler. 2000b. Genie-Gene finding in Drosophila melanogaster. Genome Res. (this issue).
22. Schultz, J., R.R. Copley, T. Doerks, C.P. Ponting, and P. Bork. 2000. SMART: A Web-based tool for the study of genetically mobile domains. Nucleic Acids Res. 28: 231-234.