A comprehensive approach to clustering of expressed human gene sequence: The Sequence Tag Alignment and Consensus Knowledge base

Genome Research

Volumn 9, Issue 11, 1999, Pages 1143-1155

  Miller, Robert T ^a   Christoffels, Alan G ^a   Gopalakrishnan, Chella ^a   Burke, John ^b   Ptitsyn, Andrey A ^a   Broveak, Tania R ^c   Hide, Winston A ^a  

^a UNIVERSITY OF THE WESTERN CAPE   (South Africa)

^b Pangea Systems   (United States)

^c Electric Genetics Observatory   (South Africa)

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNATIVE RNA SPLICING; ARTICLE; CLUSTER ANALYSIS; COMPARATIVE STUDY; EXPRESSED SEQUENCE TAG; GENE EXPRESSION; GENE SEQUENCE; GENETIC POLYMORPHISM; HUMAN; PRIORITY JOURNAL;

ALGORITHMS; CLUSTER ANALYSIS; CONSENSUS SEQUENCE; DATABASES, FACTUAL; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION; GENOME, HUMAN; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ALIGNMENT;

HOMO SAPIENS;

EID: 0032727821     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.9.11.1143     Document Type: Article

References (32)

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., M. Dubnick, A.R. Kerlavage, R. Moreno, J.M. Kelley, T.R. Utterback, J.W. Nagle, C. Fields, and J.C. Venter. 1992. Sequence identification of 2,375 human brain genes. Nature 355: 632-634.
3. 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. McConbie, and J.C. Venter. 1991. Complementary DNA Sequencing: Expressed sequence tags and human genome project. Science 252: 1651-1656.
4. Altschul, S.F., W. Gish, W. Miller, E.W. Myers, and J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
5. Boguski, M.S., and Schuler, G.D. 1995. Establishment of a transcript map. Nat. Genet. 10: 369-371.
6. Bouck, J.W., Yu, W., Gibbs, R., and Worley, K. 1999. Comparison of gene indexing databases. Trends in Genet. 15: 159-162.
7. Burke, J., H. Wang, W. Hide, and D. Davison. 1998. Alternative gene form discovery and candidate selection from gene indexing projects. Genome Res. 8: 276-290.
8. Burke, J., D. Davison, and W. Hide. 1999. d2_cluster: A validated method for clustering EST and full-length cDNA. Genome Res. (this issue).
9. Chou, A. and J. Burke. 1999. CRAWview: For viewing splicing variation, gene families, and polymorphism in clusters of ESTs and full-length sequences. Bioinformatics 15:(5) 376-381.
10. Genome Sequence Database (GIO/GSDB), National Center for Genome Research, http://www.ncgr.org.
11. Green, P. 1996. PHRAP (http://www.genome.washington.edu/uwgc/analysistools/phrap.htm, phg@u.washington.edu).
12. Hide, W., J. Burke, and D. Davison. 1994. Biological evaluation of d^{2}, an algorithm for high-performance sequence comparison. J. Comput. Biol. 1:(3) 199-215.
13. Hide, W., J. Burke, A. Christoffels, and R. Miller. 1997. A novel approach towards a consensus representation of the expressed human genome. In Genome informatics 1997 (ed. S. Miyano and T. Takagi), pp. 187-196. Universal Academy Press, Inc., Tokyo, Japan. ISSN 0919-9454.
14. Hillier, L., N. Clark, T. Dubuque, K. Elliston, M. Hawkins, M. Holman, M. Hultman, T. Kucaba, M. Le, G. Lennon et al. 1996. Generation and analysis of 280,000 human expressed sequence tags. Genome Res. 6: 807-828.
15. Houlgatte, R., R. Marriage-Samson, S. Duprat, A. Tessier, S. Bentolilal, B. Lamy, and C. Auffray. 1995. The Genexpress Index: A resource for gene discovery and the genie map of the human genome. Genome Res. 5: 272-304.
16. Huang X., M.D. Adams, H. Zhou, and A.R. Korlavage. 1999. A tool for analyzing and annotating genomic sequences. Genomics. 46: 37-45.
17. Jurka, J. 1998. Repeats in genomic DNA: Mining and meaning. Curr. Opin. Struct, Biol. 8: 333-337. http://charon.girinst.org/~server/ repbase.html.
18. Karlak, B. and W. Hide. 1998. Assessment of utility of ESTs for nucleotide diversity using available assembled alignments from dbEST, STACK v.2.0, and STACK-INDEX. In Genome informatics 1998 (ed. S. Miyano and T. Takagi) pp. 266-268. Universal Academy Press Inc., Tokyo, Japan. ISBN 0919-9454.
19. Malone K., M. Sohocki, L. Sullivan, and S. Daiger. 1999. Identifying and mapping novel retinal-expressed ESTs from humans. Mol. Vis. 5: 5.
20. Matsubara, K. and K. Okubo. 1993. Identification of new genes by systematic analysis of cDNAs and database construction. Curr. Opin. Biotechnol. 4: 672-677.
21. Muilu, J., P. Rodriguez-Tome, and A. Robinson. 1999. GenomeBuilder: Integrating external applications and databases using CORBA. Seventh International Conference on Intelligent Systems for Molecular Biology, (ed. T. Lengauer, R. Schneider, P. Bork, D. Brutlag, J. Glasgow, H.-W. Mewes, and R. Zimmer), pp. 103.
22. Okubo, K., H. Hori, R. Matuba, T. Niiyama, and K. Matsubara. 1991. A novel system for large-scale sequencing of cDNA by PCR amplification. DNA Seq. 2: 137-144.
23. Schuler, G., M. Boguski, E. Stewart, L. Stein, G. Gyapay, K. Rice, R. White, P. Rodriguez-Tome, A. Aggarwal, E. Bajorek et al. 1996. A gene map of the human genome. Science 274: 540-546.
24. 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. Comp. Appl. Biosci. 10: 671-675.
25. Sullivan L.S., J. Heckenlively, S. Bowne, J. Zuo, W. Hide, A. Gal, M. Denton, C. Inglehearn, S. Banton, and S. Daiger. 1999. Mutations in a novel retina-specific gene cause autosomal dominant retinitis pigmentosa. Nat. Genet. 22: 255-259.
26. Sutton, G., O. White, D. Adams, and A. Kerlavage. 1995. TIGR Assembler: A new tool for assembling large shotgun sequencing projects. Genome Sci. Technol. 1:(1) 9-18.
27. Tanaka, T., A. Ogiwara, I. Uchiyama, T. Takagi, Y. Yazaki, and Y. Nakamura. 1996. Construction of a normalized directionally cloned cDNA library from adult heart and analysis of 3040 clones by partial sequencing. Genomics 35: 231-235.
28. Torney, D., C. Burks, D. Davison, and K. Sirotkin. 1990a. A simple measure of sequence divergence. Los Alamos National Laboratory technical report LAUR 89-946. LANL, Los Alamos, NM.
29. 2. A measure of sequence dissimilarity. In Computers and DNA, (ed. G. Bell and T. Marr), Santa Fe Institute studies in the sciences of complexity, vol. VII. Addison-Wesley, New York, NY.
30. Vasmatzis, G., M. Essand, U. Brinkmann, B. Lee, and I. Pastan. 1998. Discovery of three genes specifically expressed in human prostate by expressed sequence tag database analysis. Proc. Natl. Acad. Sci. 95:(1) 300-304.
31. Williamson, A., K. Elliston, and J. Sturchio. 1995. The Merck Gene Index, a public resource for genomics research. J. NIH Res. 7: 61-63.
32. Wolfberg, T. and D. Landsman. 1997. A comparison of expressed sequence tags (ESTs) to human genomic sequences. Nucleic Acids Res. 25:(8) 1626-1632.