Alignment of whole genomes
作者： A. L. Delcher , S. Kasif , R. D. Fleischmann , J. Peterson , O. White
关键词:
摘要: A new system for aligning whole genome sequences is described. Using an efficient data structure called a suffix tree, the able to rapidly align containing millions of nucleotides. Its use demonstrated on two strains Mycoplasma tuberculosis, less similar species bacteria and syntenic from human chromosome 12 mouse 6. In each case it found alignment input sequences, using between 30 s 2 min computation time. From output, information single nucleotide changes, translocations homologous genes can easily be extracted. Use algorithm should facilitate analysis chromosomal regions, strain-to-strain comparisons, evolutionary comparisons genomic duplications.
oup.com
elsevier.com
paperity.org
core.ac.uk
oxfordjournals.org
jhu.edu 
swarthmore.edu 
baskent.edu.tr 参考文章(32)
William R. Pearson, Comparison of methods for searching protein sequence databases Protein Science. ,vol. 4, pp. 1145- 1160 ,(1995) , 10.1002/PRO.5560040613
Combinatorial Algorithms on Words Springer-Verlag New York, Inc.. ,(1985) , 10.1007/978-3-642-82456-2
Robert D Fleischmann, Mark D Adams, Owen White, Rebecca A Clayton, Ewen F Kirkness, Anthony R Kerlavage, Carol J Bult, Jean-Francois Tomb, Brian A Dougherty, Joseph M Merrick, Keith McKenney, Granger Sutton, Will FitzHugh, Chris Fields, Jeannine D Gocayne, John Scott, Robert Shirley, Li-lng Liu, Anna Glodek, Jenny M Kelley, Janice F Weidman, Cheryl A Phillips, Tracy Spriggs, Eva Hedblom, Matthew D Cotton, Teresa R Utterback, Michael C Hanna, David T Nguyen, Deborah M Saudek, Rhonda C Brandon, Leah D Fine, Janice L Fritchman, Joyce L Fuhrmann, NSM Geoghagen, Cheryl L Gnehm, Lisa A McDonald, Keith V Small, Claire M Fraser, Hamilton O Smith, J Craig Venter, Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. ,vol. 269, pp. 496- 512 ,(1995) , 10.1126/SCIENCE.7542800
Dan Gusfield, Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology ,(1997)
D. Lipman, W. Pearson, Rapid and sensitive protein similarity searches Science. ,vol. 227, pp. 1435- 1441 ,(1985) , 10.1126/SCIENCE.2983426
Stefan Kurtz, Reducing the space requirement of suffix trees Software - Practice and Experience. ,vol. 29, pp. 1149- 1171 ,(1999) , 10.1002/(SICI)1097-024X(199911)29:13<1149::AID-SPE274>3.0.CO;2-O
Sarah E. Valway, Maria Pia C. Sanchez, Thomas F. Shinnick, Ian Orme, Tracy Agerton, Debbie Hoy, J. Scott Jones, Harriet Westmoreland, Ida M. Onorato, An Outbreak Involving Extensive Transmission of a Virulent Strain ofMycobacterium tuberculosis New England Journal of Medicine. ,vol. 338, pp. 633- 639 ,(1998) , 10.1056/NEJM199803053381001
Kun-Mao Chao, Jinghui Zhang, James Ostell, Webb Miller, A local alignment tool for very long DNA sequences. Bioinformatics. ,vol. 11, pp. 147- 153 ,(1995) , 10.1093/BIOINFORMATICS/11.2.147
Michael S. Waterman, Introduction to Computational Biology: Maps, Sequences and Genomes ,(1995)
C. M. Fraser, J. D. Gocayne, O. White, M. D. Adams, R. A. Clayton, R. D. Fleischmann, C. J. Bult, A. R. Kerlavage, G. Sutton, J. M. Kelley, J. L. Fritchman, J. F. Weidman, K. V. Small, M. Sandusky, J. Fuhrmann, D. Nguyen, T. R. Utterback, D. M. Saudek, C. A. Phillips, J. M. Merrick, J.-F. Tomb, B. A. Dougherty, K. F. Bott, P.-C. Hu, T. S. Lucier, The minimal gene complement of Mycoplasma genitalium Science. ,vol. 270, pp. 397- 403 ,(1995) , 10.1126/SCIENCE.270.5235.397