Analysis of EST-driven gene annotation in human genomic sequence

Genome Research

Volumn 8, Issue 4, 1998, Pages 362-376

  Bailey Jr , L Charles ^a   Searls, David B ^a,b   Overton, G Christian ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b GLAXOSMITHKLINE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA;

ARTICLE; DATA BASE; GENE SEQUENCE; HUMAN; PATTERN RECOGNITION; PRIORITY JOURNAL; SEQUENCE HOMOLOGY; SEQUENCE TAGGED SITE; TECHNIQUE;

EID: 2642630755     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.8.4.362     Document Type: Article

References (41)

1. Aaronson, J.S., B. Eckman, R.A. Blevins, J.A. Borkowski, J. Myerson, S. Imran, and K.O. Elliston. 1996. Toward the development of a gene index to the human genome: An assessment of the nature of high-throughput EST sequence data. Genome Res. 6: 829-845.
2. Adams, M.D., A.R. Kerlavage, R.D. Fleischmann, R.A. Fuldner, C.J. Bult, N.H. Lee, E.F. Kirkness, K.G. Weinstock, J.D. Gocayne, O. White et al. 1995. Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence. Nature 377: 3-174.
3. 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.
4. Ansari-Lari, M.A., Y. Shen, D.M. Muzny, W. Lee, and R.A. Gibbs. 1997. Large-scale sequencing in human chromosome 12p13: Experimental and computational gene structure determination. Genome Res. 7: 268-280.
5. Antequera, F. and A. Bird. 1993. Number of CpG islands and genes in human and mouse. Proc. Natl. Acad. Sci. 90: 11995-11999.
6. Bailey, L.C., Jr., S. Fischer, J. Schug, J. Crabtree, M. Gibson, and G.C. Overton. 1998. GAIA: Framework annotation of genomic sequence. Genome Res. 8: 234-250.
7. Banfi, S., G. Borsani, E. Rossi, L. Bernard, A. Guffanti, F. Rubboli, A. Marchitiello, S. Giglio, E. Coluccia, M. Zollo et al. 1996. Identification and mapping of human cDNAs homologous to Drosophila mutant genes through EST database searching. Nature Genet. 13: 167-174.
8. Bassett, D.E., Jr., M.S. Boguski, F. Spencer, R. Reeves, M. Goebl, and P. Hieter. 1995. Comparative genomics, genome cross-referencing and XREFdb. Trends Genet. 11: 372-373.
9. 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.
10. Berget, S.M. 1995. Exon recognition in vertebrate splicing. J. Biol. Chem. 270: 2411-2414.
11. Bidaud, M.M. 1997. Banbury Cross. http://igs-server.cnrs-mrs.fr/banbury/index.html.
12. Boguski, M.S. and G.D. Schuler. 1995. ESTablishing a human transcript map. Nature Genet. 10: 369-371.
13. Boguski, M.S., T.M. Lowe, and C.M. Tolstoshev. 1993. dbEST-database for "expressed sequence tags." Nature Genet. 4: 332-333.
14. Burset, M., and R. Guigo. 1996. Evaluation of gene structure prediction programs. Genomics 34: 353-367.
15. Cerretti, D.P., T. Vanden Bos, N. Nelson, C.J. Kozlosky, P. Reddy, E. Maraskovsky, L.S. Park, S.D. Lyman, N.G. Copeland, D.J. Gilbert et al. 1995. Isolation of LERK-5: A ligand of the eph-related receptor tyrosine kinases. Mol. Immunol. 32: 1197-1205.
16. Chen, C.N., Y. Su, P. Baybayan, A. Siruno, R. Nagaraja, R. Mazzarella, D. Schlessinger, and E. Chen. 1996. Ordered shotgun sequencing of a 135 kb Xq25 YAC containing ANT2 and four possible genes, including three confirmed by EST matches. Nucleic Acids Res. 24: 4034-4041.
17. Clark, S.W., O. Staub, I.B. Clark, E.L. Holzbaur, B.M. Paschal, R.B. Vallee, and D.I. Meyer. 1994. Beta-centractin: Characterization and distribution of a new member of the centractin family of actin-related proteins. Mol. Biol. Cell 5: 1301-1310.
18. Fields, C., M.D. Adams, O. White, and J.C. Venter. 1994. How many genes in the human genome? Nature Genet. 7: 345-346.
19. Frazer, K.A., Y. Ueda, Y. Zhu, V.R. Gifford, M.R. Garofalo, N. Mohandas, C.H. Martin, M.J. Palazzolo, J.F. Cheng, and E.M. Rubin. 1997. Computational and biological analysis of 680 kb of DNA sequence from the human 5q31 cytokine gene cluster region. Genome Res. 7: 495-512.
20. Gish, W. 1997. WU-BLAST version 2.0. http://blast. wustl.edu.
21. 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.
22. Greene, J., M. Wang, Y.E. Liu, L.A. Raymond, C. Rosen, and Y.E. Shi. 1996. Molecular cloning and characterization of human tissue inhibitor of metalloproteinase 4. J. Biol. Chem. 271: 30375-30380.
23. Heiss, N.S., U.C. Rogner, P. Kioschis, B. Korn, and A. Poustka. 1996. Transcription mapping in a 700-kb region around the DXS52 locus in Xq28: Isolation of six novel transcripts and a novel ATPase isoform (hPMCA5). Genome Res. 6: 478-491.
24. Hillier, L.D., G. Lennon, M. Becker, M.F. Bonaldo, B. Chiapelli, S. Chissoe, N. Dietrich, T. DuBuque, A. Favello, W. Gish et al. 1996. Generation and analysis of 280,000 human expressed sequence tags. Genome Res. 6: 807-828.
25. Hu, R.J., M.P. Lee, T.D. Connors, L.A. Johnson, T.C. Burn, K. Su, G.M. Landes, and A.P. Feinberg. 1997. A 2.5-Mb transcript map of a tumor-suppressing subchromosomal transferable fragment from 11p15.5, and isolation and sequence analysis of three novel genes. Genomics 46: 9-17.
26. Jurka, J. and C. Pethiyagoda. 1995. Simple repetitive DNA sequences from primates: Compilation and analysis. J. Mol. Evol. 40: 120-126.
27. Jurka, J., J. Walichiewicz, and A. Milosavljevic. 1992. Prototypic sequences for human repetitive DNA. J. Mol. Evol. 35: 286-291.
28. 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.
29. Keen, G., J. Burton, D. Crowley, E. Dickinson, A. Espinosa-Lujan, E. Franks, C. Harger, M. Manning, S. March, M. McLeod et al. 1996. The Genome Sequence DataBase (GSDB): Meeting the challenge of genomic sequencing. Nucleic Acids Res. 24: 13-16.
30. Lamerdin, J.E., S.A. Stilwagen, M.H. Ramirez, L. Stubbs, and A.V. Carrano. 1996. Sequence analysis of the ERCC2 gene regions in human, mouse, and hamster reveals three linked genes. Genomics 34: 399-409.
31. 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.
32. Merck. 1996. The Merck Gene Index Project. http://www.merck.com/mrl/merck_gene_index.2.html.
33. O'Dowd, B.F., T. Nguyen, K.R. Lynch, L.F. Kolakowski, Jr., M. Thompson, R. Cheng, A. Marchese, G. Ng, H.H. Heng, and S.R. George. 1996. A novel gene codes for a putative G protein-coupled receptor with an abundant expression in brain. FEBS Lett. 394: 325-329.
34. Overton, G.C., J.S. Aaronson, J. Haas, and J. Adams. 1994. QGB: A system for querying sequence database fields and features. J. Comput. Biol. 1: 3-14.
35. Ruddy, D.A., G.S. Kronmal, V.K. Lee, G.A. Mintier, L. Quintana, R. Domingo, Jr., N.C. Meyer, A. Irrinki, E.E. McClelland, A. Fullan et al. 1997. A 1.1-Mb transcript map of the hereditary hemochromatosis locus. Genome Res. 7: 441-456.
36. Snyder, E.E. and G.D. Stormo. 1995. Identification of protein coding regions in genomic DNA. J. Mol. Biol. 248: 1-18.
37. Uberbacher, E.C., Y. Xu, and R.J. Mural. 1996. Discovering and understanding genes in human DNA sequence using GRAIL. Methods Enzymol. 266: 259-281.
38. White, O. and A.R. Kerlavage. 1996. TDB: New databases for biological discovery. Methods Enzymol. 266: 27-40.
39. Williamson, A.R., K.O. Elliston, and J.L. Sturchio. 1995. The Merck Gene Index, a public resource for genomics research. J. NIH Res. 7: 61-63.
40. Wilson, M.P. and P.W. Majerus. 1996. Isolation of inositol 1,3,4-trisphosphate 5/6-kinase, cDNA cloning and expression of the recombinant enzyme. J. Biol. Chem. 271: 11904-11910.
41. Wolfsberg, T.G. and D. Landsman. 1997. A comparison of expressed sequence tags (ESTs) to human genomic sequences. Nucleic Acids Res. 25: 1626-1632.