RAPSearch: a fast protein similarity search tool for short reads
作者： Yuzhen Ye , Jeong-Hyeon Choi , Haixu Tang
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摘要: … In the alignment between a query protein and a subject protein in the database, the longest … Therefore, in order to identify a protein in the database that is similar to the query protein, we …
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John C. Wootton, Scott Federhen, Analysis of compositionally biased regions in sequence databases. Methods in Enzymology. ,vol. 266, pp. 554- 571 ,(1996) , 10.1016/S0076-6879(96)66035-2
Peer Bork, Toby J. Gibson, Applying motif and profile searches. Methods in Enzymology. ,vol. 266, pp. 162- 184 ,(1996) , 10.1016/S0076-6879(96)66013-3
S. Karlin, S. F. Altschul, Applications and statistics for multiple high-scoring segments in molecular sequences. Proceedings of the National Academy of Sciences of the United States of America. ,vol. 90, pp. 5873- 5877 ,(1993) , 10.1073/PNAS.90.12.5873
F Meyer, D Paarmann, M D'Souza, R Olson, EM Glass, M Kubal, T Paczian, A Rodriguez, R Stevens, A Wilke, J Wilkening, RA Edwards, The Metagenomics RAST Server: A Public Resource for the Automatic Phylogenetic and Functional Analysis of Metagenomes BMC Bioinformatics. ,vol. 9, pp. 386- 386 ,(2008) , 10.1186/1471-2105-9-386
John C. Wooley, Yuzhen Ye, Metagenomics: Facts and Artifacts, and Computational Challenges* Journal of Computer Science and Technology. ,vol. 25, pp. 71- 81 ,(2010) , 10.1007/S11390-010-9306-4
, K. E. Nelson, G. M. Weinstock, S. K. Highlander, K. C. Worley, H. H. Creasy, J. R. Wortman, D. B. Rusch, M. Mitreva, E. Sodergren, A. T. Chinwalla, M. Feldgarden, D. Gevers, B. J. Haas, R. Madupu, D. V. Ward, B. W. Birren, R. A. Gibbs, B. Methe, J. F. Petrosino, R. L. Strausberg, G. G. Sutton, O. R. White, R. K. Wilson, S. Durkin, M. G. Giglio, S. Gujja, C. Howarth, C. D. Kodira, N. Kyrpides, T. Mehta, D. M. Muzny, M. Pearson, K. Pepin, A. Pati, X. Qin, C. Yandava, Q. Zeng, L. Zhang, A. M. Berlin, L. Chen, T. A. Hepburn, J. Johnson, J. McCorrison, J. Miller, P. Minx, C. Nusbaum, C. Russ, S. M. Sykes, C. M. Tomlinson, S. Young, W. C. Warren, J. Badger, J. Crabtree, V. M. Markowitz, J. Orvis, A. Cree, S. Ferriera, L. L. Fulton, R. S. Fulton, M. Gillis, L. D. Hemphill, V. Joshi, C. Kovar, M. Torralba, K. A. Wetterstrand, A. Abouellleil, A. M. Wollam, C. J. Buhay, Y. Ding, S. Dugan, M. G. FitzGerald, M. Holder, J. Hostetler, S. W. Clifton, E. Allen-Vercoe, A. M. Earl, C. N. Farmer, K. Liolios, M. G. Surette, Q. Xu, C. Pohl, K. Wilczek-Boney, D. Zhu, A catalog of reference genomes from the human microbiome. Science. ,vol. 328, pp. 994- 999 ,(2010) , 10.1126/SCIENCE.1183605
Christian E. Schafmeister, Sherry L. LaPorte, Larry J. W. Miercke, Robert M. Stroud, A designed four helix bundle protein with native-like structure. Nature Structural & Molecular Biology. ,vol. 4, pp. 1039- 1046 ,(1997) , 10.1038/NSB1297-1039
David S. Riddle, Jed V. Santiago, Susan T. Bray-Hall, Nikunj Doshi, Viara P. Grantcharova, Qian Yi, David Baker, Functional rapidly folding proteins from simplified amino acid sequences Nature Structural & Molecular Biology. ,vol. 4, pp. 805- 809 ,(1997) , 10.1038/NSB1097-805
S Altschula, Warren Gisha, Webb Millerb, E Meyersc, D Lipmana, None, Basic Local Alignment Search Tool Journal of Molecular Biology. ,vol. 215, pp. 403- 410 ,(1990) , 10.1016/S0022-2836(05)80360-2
Scott Schwartz, W James Kent, Arian Smit, Zheng Zhang, Robert Baertsch, Ross C Hardison, David Haussler, Webb Miller, Human–Mouse Alignments with BLASTZ Genome Research. ,vol. 13, pp. 103- 107 ,(2003) , 10.1101/GR.809403