A compartmentalized approach to the assembly of physical maps

Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE

Volumn , Issue , 2007, Pages 218-225

  Bozdag, Serdar ^a   Close, Timothy J ^b   Lonardi, Stefano ^a  

^a University of California ^*  (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONTIGS; GENETIC MARKERS;

CLONING;

EID: 47649107470     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBE.2007.4375568     Document Type: Conference Paper

References (32)

1. HarvEST home page. http://www.harvest-web.org/.
2. Rice physical map data. ftp://ftp.genome.arizona.edu/pub/fpc/rice/.
3. Rice BAC library home page. http://www.genome.arizona.edu/stc/rice.
4. NCBI rice unigenes home page. ftp://ftp.ncbi.nih.gov/repository/UniGene/ Oryza_sativa/.
5. TIGR rice genome sequence version 4. ftp://ftp.tigr.org/pub/data/ Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_4.0.
6. ALIZADEH, F., KARP, R. M., NEWBERG, L. A., AND WEISSER, D. K. Physical mapping of chromosomes: A combinatorial problem in molecular biology. Algorithmica 13, 1 (1995), 52-76.
7. BARBAZUK, W., BEDELL, J., AND RABINOWICZ, P. Reduced representation sequencing: a success in maize and a promise for other plant genomes. Bioessays 27, 8 (2005), 839-848.
8. BEDELL, J. A., BUDIMAN, M. A., AND et al. Sorghum genome sequencing by methylation filtration. PLoS Biol 3, 1 (2005), e13.
9. CHEN, M., PRESTING, G., AND et al. An integrated physical and genetic map of the rice genome. Plant Cell 14, 3 (Mar. 2002), 537-545.
10. DING, Y., JOHNSON, M. D., CHEN, W. Q., WONG, D., CHEN, Y. J., BENSON, S. C., LAM, J. Y., KIM, Y. M., AND SHIZUYA, H. Five-color-based high-information-content fingerprinting of bacterial artificial chromosome clones using type IIS restriction endonucleases. Genomics 74, 2 (June 2001), 142-154.
11. DING, Y., JOHNSON, M. D., COLAYCO, R., CHEN, Y. J., MELNYK, J., SCHMITT, H., AND SHIZUYA, H. Contig assembly of bacterial artificial chromosome clones through multiplexed fluorescence-labeled fingerprinting. Genomics 56, 3 (Mar. 1999), 237-246.
12. EVANS, G. A., AND LEWIS, K. A. Physical mapping of complex genomes by cosmid multiplex analysis. Proceedings of the National Academy of Sciences 86, 13 (1989), 5030-5034.
13. FASULO, D. P., JIANG, T., KARP, R. M., SETTERGREN, R., AND THAYER, E. C. An algorithmic approach to multiple complete digest mapping. Journal of Computational Biology 6, 2 (1999), 187-208.
14. GREEN, E. Strategies for the Systematic Sequencing of Complex Genomes. Nature Reviews Genetics 2 (2001), 573-583.
15. GREGORY, S., SEKHON, M., AND et al. A physical map of the mouse genome. Nature 418 (2002), 743-750. 10.1038/nature00957.
16. INTERNATIONAL HUMAN GENOME SEQUENCING CONSORTIUM. A physical map of the human genome. Nature 409 (2001), 934-941. 10.1038/35057157.
17. KRZYWINSKI, M., WALLIS, J., AND et al. Integrated and Sequence-Ordered BAC- and YAC-Based Physical Maps for the Rat Genome. Genome Res. 14, 4 (2004), 766-779.
18. KURTZ, S., PHILLIPPY, A., DELCHER, A., SMOOT, M., SHUMWAY, M., ANTONESCU, C., AND SALZBERG, S. Versatile and open software for comparing large genomes. Genome Biology 5, 2 (2004), R12.
19. LUO, M., THOMAS, C., YOU, F., HSIAO, J., OUYANG, S., BUELL, C., MALANDRO, M., MCGUIRE, P., ANDERSON, O., AND DVORAK, J. High-throughput fingerprinting of bacterial artificial chromosomes using the snapshot labeling kit and sizing of restriction fragments by capillary electrophoresis. Genomics 82 (2003), 378-389.
20. MADISHETTY, K., CONDAMINE, P., MOSCOU, M., SVENSSON, J., ZHENG, J., WANAMAKER, S., BHAT, P., RODRIGUEZ, E., WALIA, H., BOZDAG, S., REZNIK, J., LE, H., LUO, M.-C., JIANG, T., LONARDI, S., WITT, H., YOU, F., KLEINHOFS, N. S. A., COOPER, L., GILL, K., MUEHLBAUER, G., WISE, R., AND CLOSE, T. J. Towards a physical map of the barley "gene space". in preparation, 2007.
21. MARRA, M., KUCABA, T., AND et al. A map for sequence analysis of the Arabidopsis thaliana genome. Nat Genet 22, 3 (July 1999), 265-270.
22. NELSON, W., BHARTI, A., BUTLER, E., WEI, F., FUKS, G., KIM, H., WING, R., MESSING, J., AND SODERLUND, C. Whole-Genome Validation of High-Information-Content Fingerprinting. Plant Physiol. 139, 1 (2005), 27-38.
23. NELSON, W., AND SODERLUND, C. Software for restriction fragment physical maps. In The Handbook of Genome Mapping: Genetic and Physical Mapping, K. Meksem and G. Kahl, Eds. Wiley-VCH, 2005, pp. 285-306.
24. OLSON, M., DUTCHIK, J., GRAHAM, M., BRODEUR, G., HELMS, C., FRANK, M., MACCOLLIN, M., SCHEINMAN, R., AND FRANK, T. Random-Clone Strategy for Genomic Restriction Mapping in Yeast. PNAS 83, 20 (1986), 7826-7830.
25. REN, C., LEE, M., YAN, B., DING, K., COX, B., ROMANOV, M., PRICE, J., DODGSON, J., AND ZHANG, H. A BAC-Based Physical Map of the Chicken Genome. Genome Res. 13, 12 (2003), 2754-2758.
26. SCALABRIN, S., MORGANTE, M., AND MEYERS, B. Mapping and Sequencing Complex Genomes: Let's get Physical! Nature Review vs Genetics 5 (2004), 578-588. 10.1038/nrg1404.
27. SODERLUND, C., HUMPHRAY, S., DUNHAM, A., AND FRENCH, L. Contigs Built with Fingerprints, Markers, and FPC V4.7. Genome Res. 10, 11 (2000), 1772-1787.
28. SULSTON, J., MALLETT, F., STADEN, R., DURBIN, R., HORSNELL, T., AND COULSON, A. Software for genome mapping by fingerprinting techniques. Comput. Appl. Biosci. 4, 1 (1988), 125-132.
29. TAO, Q., CHANG, Y., WANG, J., CHEN, H., ISLAM-FARIDI, M., SCHEURING, C., WANG, B., STELLY, D., AND ZHANG, H. Bacterial Artificial Chromosome-Based Physical Map of the Rice Genome Constructed by Restriction Fingerprint Analysis. Genetics 158, 4 (2001), 1711-1724.
30. WARREN, R. L., VARABEI, D., AND et al. Physical map-assisted whole-genome shotgun sequence assemblies. Genome Res 16, 6 (June 2006), 768-775.
31. YU, Y., TOMKINS, J., WAUGH, R., FRISCH, D., KUDRNA, D., KLEINHOFS, A., BRUEGGEMAN, R., MUEHLBAUER, G., WISE, R., AND WING, R. A bacterial artificial chromosome library for barley (Hordeum vulgare L.) and the identification of clones containing putative resistance genes. Theor. Appl. Genet. 101 (2000) 1093-1099.
32. ZHENG, J., SVENSSON, J. T., MADISHETTY, K., CLOSE, T. J., JIANG, T., AND LONARDI, S. OligoSpawn: a software tool for the design of overgo probes from large unigene datasets. BMC Bioinformatics 7, 7(2006).