GAIA: Framework annotation of genomic sequence

Genome Research

Volumn 8, Issue 3, 1998, Pages 234-250

  Bailey Jr , L Charles ^a   Fischer, Stephen ^a   Schug, Jonathan ^a   Crabtree, Jonathan ^a   Gibson, Mark ^a   Overton, G Christian ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; AUTOANALYSIS; COMPUTER PROGRAM; DATA BASE; GENE SEQUENCE; INFORMATION PROCESSING; INTERNET; PRIORITY JOURNAL;

EID: 2642714164     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.8.3.234     Document Type: Article

References (32)

1. 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.
2. Bailey, L.C., Jr., D.B. Searls, and G.C. Overton. 1998. EST-driven gene annotation in human genomic sequence. Genome Res. (in press).
3. Bedian, V., T. Adams, E.A. Geiger, L.C. Bailey, and D.L. Gasser. 1997. A gene belonging to the Sm family of snRNP core proteins maps within the mouse MHC. Immunogenetics 46: 427-430.
4. Buneman, P., S.B. Davidson, K. Hart, G.C. Overton, and L. Wong. 1994. A data transformation system for biological data sources. In 21st international conference on very large data bases, pp. 158-169. Morgan-Kaufmann Publishers, San Mateo, CA.
5. Burge, C. and S. Karlin. 1997. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268: 78-94.
6. Burset, M. and R. Guigo. 1996. Evaluation of gene structure prediction programs. Genomics 34: 353-367.
7. Charlebois, R.L., T. Gaasterland, M.A. Ragan, W.F. Doolittle, and C.W. Sensen. 1996. The Sulfolobus solfataricus P2 genome project. FEBS Lett. 389: 88-91.
8. Crabtree, J., S. Fischer, M. Gibson, and G.C. Overton. 1998. bioWidgets: Reusable visualization components for bioinformatics. In Molecular biology database (ed. S. Letovsky). Kluwer Academic Publishers, Dordrecht, The Netherlands.
9. DDBJ/EMBL/GenBank. 1996. DDBJ/EMBL/GenBank Feature table: Definition.
10. GCG (Genetics Computer Group). 1996. Program manual for the Wisconson sequence analysis package, version 9.0. Genetics Computer Group, Madison, WI.
11. Gong, W., B.S. Emanuel, J. Collins, D.H. Kim, Z. Wang, F. Chen, G. Zhang, B. Roe, and M.L. Budarf. 1996. A transcription map of the DiGeorge and velo-cardio-facial syndrome minimal critical region on 22q11. Hum. Mol. Genet. 5: 789-800.
12. Harger, C., M. Skupski, E. Allen, C. Clark, D. Crowley, E. Dickinson, D. Easley, A. Espinosa-Lujan, A. Farmer, C. Fields et al. 1997. The Genome Sequence DataBase version 1.0 (GSDB): From low pass sequences to complete genomes. Nucleic Acids Res. 25: 18-23.
13. Harris, N.L. 1997. Genotator. A workbench for sequence annotation. Genome Res. 7: 754-762.
14. Helt, G. 1996. Drosophila Genome Browser Prototype. http:// fruitfly.berkeley.edu/javademos/GenomeBrowser.html
15. Jurka, J. and C. Pethiyagoda. 1995. Simple repetitive DNA sequences from primates: compilation and analysis. J. Mol. Evol. 40: 120-126.
16. Jurka, J., J. Walichiewicz, and A. Milosavljevic. 1992. Prototypic sequences for human repetitive DNA. J. Mol. Evol. 35: 286-291.
17. Jurka, J., P. Klonowski, V. Dagman, and P. Pelton. 1996. CENSOR - A program for identification and elimination of repetitive elements from DNA sequences. Comput. Chem. 20: 119-121.
18. Makalowski, W., J. Zhang, and M.S. Boguski. 1996. Comparative analysis of 1196 orthologous mouse and human full-length mRNA and protein sequences. Genome Res. 6: 846-857.
19. Milosavljevic, A. and J. Jurka. 1993. Discovering simple DNA sequences by the algorithmic significance method. Comput. Appl. Biosci. 9: 407-411.
20. NCGR (National Center for Genome Resources). 1996. Genome Sequence DataBase Schema (GSDB) Version 1.0. Santa Fe, NM.
21. Ouzounis, C., P. Bork, G. Casari, and C. Sander. 1995. New protein functions in yeast chromosome VIII. Protein Sci. 4: 2424-2428.
22. Overton, G.C., J. Aaronson, J. Haas, and J. Adams. 1994. QCB: A system for querying sequence database fields and features. J. Comp. Biol. 1: 3-13.
23. Pangea Systems, Inc. 1997. GeneWorld 2.5. http://www. panbio.com/3_product/geneworld.htm
24. Scharf, M., R. Schneider, G. Casari, P. Bork, A. Valencia, C. Ouzounis, and C. Sander. 1994. GeneQuiz: A workbench for sequence analysis. Intell. Systems Mol. Biol. 2: 348-353.
25. Schug, J. and G.C. Overton. 1997. TESS: Transcription Element Search Software on the WWW. Technical Report CBIL-TR-1997-1001. Computational Biology and Informatics Laboratory, School of Medicine, University of Pennsylvania, Philadelphia, PA.
26. Searls, D.B. 1995. bioTk: Componentry for genome informatics graphical user interfaces. Gene 163: GC1-16.
27. Smith, S.W., R. Overbeek, C.R. Woese, W. Gilbert, and P.M. Gillevet. 1994. The genetic data environment an expandable GUI for multiple sequence analysis. Comput. Appl. Biosci. 10: 671-675.
28. Tomb, J.F., O. White, A.R. Kerlavage, R.A. Clayton, G.G. Sutton, R.D. Fleischmann, K.A. Ketchum, H.P. Klenk, S. Gill, B.A. Dougherty et al. 1997. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 388: 539-547.
29. Uberbacher, E. et al. 1997. The genome channel. http:// compbio.ornl.gov/CoLab/channel/index.html
30. Uberbacher, E.C., Y. Xu, and R.J. Mural. 1996. Discovering and understanding genes in human DNA sequence using GRAIL. Meth. Enzymol. 266: 259-281.
31. Wolfsberg, T., B.F. Ouellette, and J. Kans. 1997. Sequin. http://www.ncbi.nlm.nih.gov/Sequin/
32. Zhang, J. and T.L. Madden. 1997. PowerBLAST: A new network BLAST application for interactive or automated sequence analysis and annotation. Genome Res. 7: 649-656.