A clustering method for repeat analysis in DNA sequences

Genome Biology

Volumn 2, Issue 8, 2001, Pages

  Volfovsky, Natalia ^a   Haas, Brian J ^a   Salzberg, Steven L ^a  

^a J CRAIG VENTER INSTITUTE   (United States)

Author keywords

Bacterial Artificial Chromosome; Merging Procedure; Partition Point; Repeat Class; Suffix Tree

Indexed keywords

ARABIDOPSIS THALIANA; ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; DNA SEQUENCE; MICROBIAL GENOME; NONHUMAN; RICE; SOFTWARE; ALGORITHM; ARABIDOPSIS; BACTERIAL GENOME; BIOLOGY; CLUSTER ANALYSIS; COMPUTER PROGRAM; GENETICS; GENOME; GENOMICS; METHODOLOGY; MOLECULAR GENETICS; NEISSERIA MENINGITIDIS; NUCLEIC ACID DATABASE; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE; SENSITIVITY AND SPECIFICITY;

ALGORITHMS; ARABIDOPSIS; BASE SEQUENCE; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; GENOME, BACTERIAL; GENOME, PLANT; GENOMICS; MOLECULAR SEQUENCE DATA; NEISSERIA MENINGITIDIS; ORYZA SATIVA; REPETITIVE SEQUENCES, NUCLEIC ACID; SENSITIVITY AND SPECIFICITY; SOFTWARE;

EID: 0035230042     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2001-2-8-research0027     Document Type: Article

References (28)

1. Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, et al: The genome sequence of Drosophila melanogaster. Science. 2000, 287: 2185-2195. 10.1126/science.287.5461.2185. DOI: 10.1126/science.287.5461.2185
2. The Arabidopsis Genome Initiative: Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000, 408: 796-815. 10.1038/35048692. DOI: 10.1038/35048692
3. Leung M-Y, Blaisdell BE, Burge C, Karlin S: An efficient algorithm for identifying matches with errors in multiple long molecular sequences. J Mol Biol. 1991, 221: 1367-1378. 10.1016/0022-2836(91)80131-D. DOI: 10.1016/0022-2836(91)90938-3
4. Agarwal P, States DJ: The Repeat Pattern Toolkit (RPT): analyzing the structure and evolution of the C. elegans genome. In Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, ISMB 94, 1-9. Menlo Park, CA: AAAI Press,. 1994
5. Kannan SK, Myers EW: An algorithm for locating nonoverlapping regions of maximal alignment score. SIAM J Comput. 1996, 25: 648-662. DOI: 10.1137/S0097539794262677
6. Benson G: Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999, 27: 573-580. 10.1093/nar/27.2.573. DOI: 10.1093/nar/27.2.573
7. RepeatMasker. [http://ftp.genome.washington.edu/RM/RepeatMasker.html]
8. Bedell JA, Korf I, Gish W: MaskerAid: a performance enhancement to RepeatMasker. Bioinformatics. 2000, 16: 1040-1041. 10.1093/bioinformatics/16.11.1040. DOI: 10.1093/bioinformatics/16.11.1040
9. Gish W, States DJ: Identification of protein coding regions by database similarity search. Nat Genet. 1993, 3: 266-272. DOI: 10.1038/ng0393-266
10. Washington University School of Medicine: Index of /blast/blast. [http://blast.wustl.edu/blast]
11. Delcher AL, Kasif S, Fleischmann RD, Peterson J, White O, Salzberg SL: Alignment of whole genomes. Nucleic Acids Res. 1999, 27: 2369-2376. 10.1093/nar/27.11.2369. DOI: 10.1093/nar/27.11.2369
12. Kurtz S, Schleiermacher C: REPuter - fast computation of maximal repeats in complete genomes. Bioinformatics. 1999, 15: 426-427. 10.1093/bioinformatics/15.5.426. DOI: 10.1093/bioinformatics/15.5.426
13. Kurtz S, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R: Computation and visualization of degenerate repeats in complete genomes. In Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology. 2000, 228-238. Menlo Park, CA: AAAI-Press,
14. TIGR software tools. [http://www.tigr.org/softlab/]
15. Bult CJ, White O, Olsen GJ, Zhou L, Fleischmann RD, Sutton GG, Blake JA, FitzGerald LM, Clayton RA, Gocayne JD, et al: Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science. 1996, 273: 1058-1073. DOI: 10.1126/science.273.5278.1058
16. Fraser CM, Norris SJ, Weinstock GM, White O, Sutton G, Clayton R, Dodson R, Gwinn M, Hickey E, Ketchum KA, et al: Complete genomic sequence of Treponema pallidum, the syphilis spirochete. Science. 1998, 281: 375-388. 10.1007/s004410050434. DOI: 10.1126/science.281.5375.375
17. Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Nelson WC, Ketchum KA, et al: Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima. Nature. 1999, 399: 323-329. 10.1038/20601. DOI: 10.1038/20601
18. Read TD, Brunham RC, Shen C, Gill SR, Heidelberg JF, White O, Hickey EK, Peterson J, Utterback T, Berry K, et al: Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39. Nucleic Acids Res. 2000, 28: 1397-1406. 10.1093/nar/28.6.1397. DOI: 10.1093/nar/28.6.1397
19. Tomb JF, White O, Kerlavage AR, Clayton RA, Sutton GG, Fleischmann RD, Ketchum KA, Klenk HP, Gill SR, Dougherty BA, et al: The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature. 1997, 388: 539-547. 10.1038/41483. DOI: 10.1038/41483
20. Tettelin H, Saunders NJ, Heidelberg J, Jeffries AC, Nelson KE, Eisen JE, Ketchum KA, Hood DW, Peden JF, Dodson RJ, et al: Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. Science. 2000, 287: 1809-1815. 10.1126/science.287.5459.1809. DOI: 10.1126/science.287.5459.1809
21. Nierman W, Feldblyum TV, Laub MT, Paulsen IT, Nelson KE, Eisen J, Heidelberg JF, Alley MRK, Ohta N, Maddock JR, et al: Complete genome sequence of Caulobacter crescentus. Proc Natl Acad Sci USA. 2001, 98: 4136-4141. 10.1073/pnas.061029298. DOI: 10.1073/pnas.061029298
22. Mao L, Wood TC, Yu Y, Budiman MA, Tomkins J, Woo S, Sasinowski M, Presting G, Frisch D, Goff S, et al: Rice transposable elements: a survey of 73,000 sequence-tagged-connectors. Genome Res. 2000, 10: 982-990. 10.1101/gr.10.7.982. DOI: 10.1101/gr.10.7.982
23. Clemson University rice BAC end database. [http://www.genome.clemson.edu/projects/rice/rice:bac_end]
24. Gusfield D: Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology. New York: Cambridge University Press,. 1997 DOI: 10.1017/CBO9780511574931
25. AtRepBase. [http://nucleus.cshl.org/protarab/AtRepBase.htm]
26. Arabidopsis gene sequence database. [http://www.tigr.org/tdb/e2k1/ath1/ath1.shtml]
27. Yuan Q, Liang F, Hsiao J, Zismann V, Benito M-I, Quackenbush J, Wing R, Buell R: Anchoring of rice BAC clones to the rice genetic map in silico. Nucleic Acids Res. 2000, 28: 3636-3641. 10.1093/nar/28.18.3636. DOI: 10.1093/nar/28.18.3636
28. Oryza sativa repeat database search. [http://www.tigr.org/tdb/rice/blastsearch.shtml]