Efficient selection of unique and popular oligos for large EST databases

Bioinformatics

Volumn 20, Issue 13, 2004, Pages 2101-2112

  Zheng, Jie ^a   Close, Timothy J ^b   Jiang, Tao ^a   Lonardi, Stefano ^a  

^a University of California Riverside   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE; PRIMER DNA;

ARTICLE; BARLEY; BASE PAIRING; COMPUTER SIMULATION; COMPUTER SYSTEM; CONTROLLED STUDY; DNA MICROARRAY; EXPRESSED SEQUENCE TAG; GENE FREQUENCY; GENE LIBRARY; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC ANALYSIS; GENETIC DATABASE; GENETIC ENGINEERING; GENETIC IDENTIFICATION; GENETIC SCREENING; GENETIC SELECTION; MOLECULAR CLONING; MOLECULAR PROBE; NONHUMAN; ONLINE SYSTEM; PLANT SEED; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL;

HORDEUM VULGARE SUBSP. VULGARE;

EID: 4544268787     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bth210     Document Type: Article

References (29)

1. Adams,M.D., Kelley,J.M., Gocayne,J.D., Dubnick,M., Polymeropoulos,M.H., Xiao,H., Merril,C.R., Wu,A., Olde,B., Moreno,R.F. et al. (1991) Complementary DNA sequencing: expressed sequence tags and human genome project. Science, 252, 1651-1656.
2. Apostolico,A., Bock,M.E. and Lonardi,S. (2003) Monotony of surprise and large-scale quest for unusual words (extended abstract). In Myers,G., Hannenhalli,S., Istrail,S., Pevzner,P. and Waterman,M. (eds), Proceedings of Research in Computational Molecular Biology (RECOMB), Washington, DC, April. J. Comput. Biol., 10, 3-4, 283-311.
3. Apostolico,A., Gong,F. and Lonardi,S. (2004) Verbumculus and the discovery of unusual words. J. Comput. Sci. Technol., 19, 22-41.
4. Bailey,T.L. and Elkan,C. (1995) Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Machine Learn., 21, 51-80.
5. Barakat,A., Carels,N. and Bernardi,G. (1997) The distribution of genes in the genomes of gramineae. Proc. Natl Acad. Sci., USA, 94, 6857-6861.
6. Boguski,M., Lowe,T. and Tolstoshev,C. (1993) dbEST - database for "expressed sequence tags". Nat. Genet., 4, 332-333.
7. Buhler,J. and Tompa,M. (2002) Finding motifs using random projections. J. Comput. Biol., 9, 225-242.
8. Close,T., Wing,R., Kleinhofs,A. and Wise,R. (2001) Genetically and physically anchored EST resources for barley genomics. Barley Genet. Newslett., 31, 29-30.
9. Cormen,T.H., Leiserson,C.E. and Rivest,R.L. (1990) Introduction to Algorithms. MIT Press, Cambridge, MA.
10. Eskin,E. and Pevzner,P.A. (2002) Finding composite regulatory patterns in DNA sequences. Proceedings of the International Conference on Intelligent Systems for Molecular Biology. AAAI press, Menlo Park, CA, pp. S181-S188.
11. Garey,M.R. and Johnson,D.S. (1979) Computers and Intractability: a Guide to the Theory of NP-completeness. Freeman, New York.
12. Han,C., Sutherland,R., Jewett,P., Campbell,M., Meincke,L., Tesmer,J., Mundt,M., Fawcett,J., Kim,U., Deaven,L. and Doggett,N. (2000) Construction of a BAC contig map of chromosome 16q by two-dimensional overgo hybridization. Genome Res., 104, 714-721.
13. Hertz,G.Z. and Stormo,G.D. (1999) Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics, 15, 563-577.
14. Huang,X. and Madan,A. (1999) CAP3: a DNA sequence assembly program. Genome Res., 9, 868-877.
15. Jonassen,I. (1997) Efficient discovery of conserved patterns using a pattern graph. Comput. Appl. Biosci., 13, 509-522.
16. Jonassen,I., Collins,J.F. and Higgins,D.G. (1995) Finding flexible patterns in unaligned protein sequences. Protein Sci., 4, 1587-1595.
17. Keich,U. and Pevzner,P.A. (2002) Finding motifs in the twilight zone. Annual International Conference on Computational Molecular Biology, Washington, DC, April, pp. 195-204.
18. Lawrence,C.E., Altschul,S.F., Boguski,M.S., Liu,J.S., Neuwald,A.F. and Wootton,J.C. (1993) Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science, 262, 208-214.
19. Li,F. and Stormo,G.D. (2001) Selection of optimal DNA oligos for gene expression arrays. Bioinformatics, 17, 1067-1076.
20. Michalek,W., Weschke,W., Pleissner,K. and Graner,A. (2002) EST analysis in barley defines a unigene set comprising 4,000 genes. Theor. Appl. Genet., 104, 97-103.
21. Neuwald,A., Liu,J. and Lawrence,C. (1995) Gibbs motif sampling: detecting bacterial outer membrane protein repeats. Protein Sci., 4, 1618-1632.
22. Pevzner,P.A. and Sze,S.-H. (2000) Combinatorial approaches to finding subtle signals in DNA sequences. Proceedings of the International Conference on Intelligent Systems for Molecular Biology. AAAI press, Menlo Park, CA, pp. 269-278.
23. Rahmann,S. (2002) Rapid large-scale oligonucleotide selection for microarrays. Proceedings of the First IEEE Computer Society Bioinformatics Conference (CSB'02). IEEE Press, Los Alamitos, pp. 54-63.
24. Rigoutsos,I. and Floratos,A. (1998) Combinatorial pattern discovery in biological sequences: the TEIRESIAS algorithm. Bioinformatics, 14, 55-67.
25. Rouillard,J.-M., Herbert,C.J. and Zuker,M. (2002) Oligoarray: genome-scale oligonucleotide design for microarrays. Bioinformatics, 18, 486-487.
26. Swofford,D. (2002) PAUP: Phylogenetic Analysis Using Parsimony version 4.0 beta 10. Sinauer Associates, Sunderland, Massachusetts.
27. Tompa,M. and Buhler,J. (2001) Finding motifs using random projections. Annual International Conference on Computational Molecular Biology, Montreal, Canada, April, ACM Press, NY, pp. 67-74.
28. Wesselink,J.-J., de la Iglesia,B., James,S.A., Dicks,J.L., Roberts,I.N. and Rayward-Smith,V.J. (2002) Determining a unique defining DNA sequence for yeast species using hashing techniques. Bioinformatics, 18, 1004-1010.
29. Yu, Y., Tomkins,J.P., Waugh,R., Frisch,D.A., Kudrna,D., Kleinhofs,A., Brueggeman,R.S., Muehlbauer,G.J., Wise,R.P. and Wing,R.A. (2000) A bacterial artificial chromosome library for barley (Hordeum vulgare L.) and the identification of clones containing putative resistance genes. Theor. Appl. Genet., 101, 1093-1099.