MEGAN analysis of metagenomic data

作者: D. H. Huson , A. F. Auch , J. Qi , S. C. Schuster

DOI: 10.1101/GR.5969107

关键词: FosmidDNA sequencingSet (abstract data type)GenomicsBiologyData setMetagenomicsGeneticsLowest common ancestorPhylogenetic treeComputational biology

摘要: … version of MEGAN and applied the LCA algorithm to compute … Here we provide details of the MEGAN analysis, using a bit-… The LCA algorithm assigned 50,093 reads to taxa, and 2086 …

参考文章(26)
Achim Quaiser, Torsten Ochsenreiter, Christa Lanz, Stephan C. Schuster, Alexander H. Treusch, Jürgen Eck, Christa Schleper, Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics. Molecular Microbiology. ,vol. 50, pp. 563- 575 ,(2003) , 10.1046/J.1365-2958.2003.03707.X
CL HICKS, R. KINOSHITA, PW LADDS, Pathology of melioidosis in captive marine mammals Australian Veterinary Journal. ,vol. 78, pp. 193- 195 ,(2000) , 10.1111/J.1751-0813.2000.TB10593.X
Jennifer B. Hughes Martiny, Brendan J.M. Bohannan, James H. Brown, Robert K. Colwell, Jed A. Fuhrman, Jessica L. Green, M. Claire Horner-Devine, Matthew Kane, Jennifer Adams Krumins, Cheryl R. Kuske, Peter J. Morin, Shahid Naeem, Lise Øvreås, Anna-Louise Reysenbach, Val H. Smith, James T. Staley, Microbial biogeography : putting microorganisms on the map Nature Reviews Microbiology. ,vol. 4, pp. 102- 112 ,(2006) , 10.1038/NRMICRO1341
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
Edward F DeLong, None, Microbial community genomics in the ocean Nature Reviews Microbiology. ,vol. 3, pp. 459- 469 ,(2005) , 10.1038/NRMICRO1158
Oded Béja, Elena N Spudich, John L Spudich, Marion Leclerc, Edward F DeLong, None, Proteorhodopsin phototrophy in the ocean Nature. ,vol. 411, pp. 786- 789 ,(2001) , 10.1038/35081051
D. Meldrum, Automation for Genomics, Part Two: Sequencers, Microarrays, and Future Trends Genome Research. ,vol. 10, pp. 1288- 1303 ,(2000) , 10.1101/GR.157400
Steven J Hallam, Nik Putnam, Christina M Preston, John C Detter, Daniel Rokhsar, Paul M Richardson, Edward F DeLong, None, Reverse methanogenesis: testing the hypothesis with environmental genomics. Science. ,vol. 305, pp. 1457- 1462 ,(2004) , 10.1126/SCIENCE.1100025
Helen L. Steele, Wolfgang R. Streit, Metagenomics: Advances in ecology and biotechnology Fems Microbiology Letters. ,vol. 247, pp. 105- 111 ,(2005) , 10.1016/J.FEMSLE.2005.05.011