Rapid in silico cloning of genes using expressed sequence tags (ESTs)

Biotechnology Annual Review

Volumn 5, Issue , 2000, Pages 25-44

  Gill, Robert W ^a   Sanseau, Philippe ^a  

^a GLAXOSMITHKLINE   (United Kingdom)

Author keywords

EST database; Expressed sequence tags; Sequence tags sites; Tentative human consensus

Indexed keywords

COMPLEMENTARY DNA;

COMPUTER MODEL; CONSENSUS SEQUENCE; DATA BASE; DNA LIBRARY; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; GENE EXPRESSION; GENE MAPPING; GENETIC POLYMORPHISM; GENETIC TRANSCRIPTION; HUMAN; HUMAN CHROMOSOME; HUMAN GENOME; MOLECULAR CLONING; MULTIGENE FAMILY; NUCLEOTIDE SEQUENCE; REVIEW; ANIMAL; COMPUTER PROGRAM; FACTUAL DATABASE; GENE LIBRARY; GENETIC DISORDER; GENETICS; GENOME; METHODOLOGY; MOLECULAR GENETICS; MOUSE;

ANIMALS; BASE SEQUENCE; CLONING, MOLECULAR; CONSERVED SEQUENCE; DATABASES, FACTUAL; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION; GENE LIBRARY; GENETIC DISEASES, INBORN; GENOME, HUMAN; HUMANS; MICE; MOLECULAR SEQUENCE DATA; POLYMORPHISM, GENETIC; SOFTWARE;

EID: 0033648987     PISSN: 13872656     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S1387-2656(00)05031-6     Document Type: Article

References (30)

1. Wilcox AS, Khan AS, Hopkins JA and Sikela JM. Use of 3′ untranslated sequences of human cDNAs for rapid chromosome assignment and conversion to STSs: implications for an expression map of the genome. Nucl Acid Res 1991;19:1837-1843.
2. Adams MD, Dubnick M, Kerlavage AR, Moreno R, Kelley JM, Utterback TR, Nagle JW, Fields C and Venter JC. Sequence identification of 2,375 human brain genes. Nature 1992;355:632-634.
3. Kalogeropoulos A. Linguistic analysis of chromosome III DNA sequence of Saccharomyces cerevisiae. Yeast 1973;9:889-905.
4. Williamson AR, Elliston KO and Sturchio JL. The Merck Gene Index, a public resource for genomics research. J NIH 1995;7:61-63.
5. Benson D, Boguski MS, Lipman D and Ostell J. GenBank. Nucl Acid Res 1994;22:3441-3444.
6. Boguski MS, Lowe TM and Tolstohev CM. dbEST: database for 'Expressed Sequence tags'. Nature Genet 1993;4:332-333.
7. Lennon GG, Auffray C, Polymeropoulos M and Soares MB. The IMAGE Consortium: An Integrated Molecular Analysis of Genomes and their Expression. Genomics 1996;33:151-152.
8. Soares MB, Bonaldo M, Jelene P, Su L, Lawton L and Efstratiadis A. Construction and characterisation of a normalized cDNA library. Proc Natl Acad USA 1994;91:9228-9232.
9. Altschul SF, Gish W, Miller W, Myers EW and Lipman DJ. Basic local alignment search tool. J Molec Biol 1990;215:403-410.
10. Collins F and Gallas D. A new five-year plan for the US Human Genome Project. Science 1993;262:43-46.
11. Boguski MS and Schuler GD. ESTblasting a human transcript map. Nature Genet 1995;10:369-371.
12. Schuler GD, Boguski MS, Stewart EA, Stein LD, Gyapay G, Rice K, White RE, Rodriguez-Tome P, Aggarwal A, Bajorek E, Bentolila S, Birren BB, Butler A, Castle AB, Chiannilkulchai N, Chu A, Clee C, Cowles S, Day PJ, Dibling T, Drouot N, Dunham I, Duprat S, East C, Edwards C, Fan JB, Fang N, Fizames C, Garett C, Green L, Hadley D, Harris M, Harrison P, Brady S, Hicks A, Holloway E, Hui L, Hussain S, Louis-Dit-Sully C, Ma J, MacGilvery A, Mader C, Maratukulam A, Matise TC, McKusick KB, Morissette J, Mungall A, Muselet D, Nusbaum HC, Page DC, Peck A, Perkins S, Piercy M, Qin F, Quackenbush J, Ranby S, Reif T, Rozen S, Sanders C, She X, Silva J, Slonim DK, Soderlun C, Sun WL, Tabar P, Thangarajah T, Vega-Czarny N, Vollrath D, Voyticky S, Wilmer T, Wu X, Adams MD, Auffray C, Walter NAR, Brandon R, Dehejia A, Goodfellow PN, Houlgatte R, Hudson JR, Ide SE, Iorio KR, Lee WY, Seki N, Nagase T, Ishikawa K, Nomura N, Phillips C, Polymeropoulos, MH, Sandusky M, Schmitt K, Berry R, Swanson K, Torres R, Venter JC, Sikela JM, Beckman JS, Weissenbach J, Myers RM, Cox DR, James MR, Bentley D, Deloukas P, Lander ES and Hudson TJ. A gene map of the human genome. Science 1996;274:540-546.
13. Gill RW, Hodgman TC, Littler CB, Oxer MD, Montgomery DS, Taylor S and Sanseau P. A new dynamic tool to perform assembly of Expressed Sequence Tags (ESTs). Comp Appl in Biosi 1997;13:453-457.
14. Lipman DJ and Pearson WR. Improved tools for biological sequence analysis. Science 1985;227:1438-1141.
15. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, and Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acid Res 1997;25:3389-3402.
16. Knuth DE. The art of computer programming. In: Addison-Wesley (ed) vol 3. London: 1972.
17. Etzold T, Ulyanov A and Argos P. SRS: Information Retrieval System for Molecular Biology Data Banks. Meth Enzymol 1996;266:114-135.
18. Etzold T and Argos P. SRS an indexing and retrieval tool for flat file data libraries. Comp Appl Biosci 1993;9:49-57.
19. Etzold T and Argos P. Transforming a set of biological flat file libraries to a fast access network. Comp Appl Biosci 1993;9:59-64.
20. Staden R. An improved sequence handling package that runs on the Apple Macinthosh. Comp Appl Biosci 1990;6:387-393.
21. Roses AD. ApoE Alzheimer diseases: a model of gene mutations and susceptibility polymorphisms for complex psychiatric diseases. Am J Med Gen 1998;81:49-57.
22. Blacker D, Wilcox MA, Laird NM, Rodes L, Horvath SM, Go RCP, Perry R, Watson Jr B, Bassett SS, McInnis MG, Albert MS, Hyman BT and Tanzi RE. Alpha-2 macroglobulin is genetically associated with Alzheimer disease. Nature Genet 1998;19:357-360.
23. Chakravarti A. It's raining SNPs, hallelujah? Nature Genetics 1998;19:216-217.
24. Fannon MR. Gene expression in normal and disease states-identification of therapeutic targets. Trends Biotechnol 1996;14:294-298.
25. Audic S and Claverie JM. The significance of digital gene expression profiles. Genome Res 1997;7:986-995.
26. Okubo K, Itoh K, Fukushima A, Yoshii J and Matsubara K. Monitoring cell physiology by expression profiles and discovering cell type-specific genes by compiled expression profiles. Genomics 1995;30:178-186
27. Lee NH, Weinstock KG, Kirkness EF, Earle-Hughes JA, Fuldner RA, Marmaros S, Glodek A, Gocayne JD, Adams MD, Kerlavage AR and Venter JC. Comparative expressed-tag analysis of differential gene expression profiles in PC-12 cells before and after nerve growth factor treatment. Proc Natl Acad Sci USA 1995;92:8303-8307.
28. Mc Donald T, Wang R, Bailey W, Xie G, Chen F, Caskey CT and Liu Q. Identification and cloning of an orphan G protein-coupled receptor of the glycoprotein hormone receptor subfamily. Biochem Biophys Res Commun 1998;247:266-270.
29. Banfi S, Borsani G, Rossi E, Bernard L, Guffanti A, Rubboli F, Marchitiello A, Giglio S, Coluccia E, Zollo M, Zuffardi O and Ballabio A. Identification and mapping of human cDNAs homologous to Drosophila mutant genes through EST database searching. Nature Genet 1996;13:167-174.
30. Hillier LD. Generation and analysis of 280,000 human expressed sequence tags. Genome Res 1996;6:807-828.