MEGAN

Infobox Software
name = MEGAN



caption =
developer = Daniel Huson et al.
latest release version = 2beta8
latest release date = 2008
latest preview version =
latest preview date =
operating system = Windows, Linux, Mac OS X
platform =
genre = Bioinformatics
license = free use, but not open source
website = http://www-ab.informatik.uni-tuebingen.de/software/megan

MEGAN ("MEtaGenome ANalyzer") is a computer program that allows optimized analysis of large metagenomic datasets. [cite journal | last = Huson | first = H. | authorlink = | coauthors = A. Auch, Ji Qi, and S. C. Schuster | title = MEGAN Analysis of Metagenomic Data | journal = Genome Research | volume = 17
issue = | pages = 377–386 | publisher = Cold Spring Harbor Laboratory Press | location = Woodbury, New York | date = 2007 | url = http://www.genome.org/cgi/reprint/gr.5969107v1 | doi = | id = | accessdate = 2008-04-03 ]

Metagenomics is the analysis of the DNA and RNA sequences from a usually uncultured environmental sample. A large term goal of most metagenomics is to inventory and measure the extent and the role of microbial biodiversity in the ecosystem due to discoveries that the diversity of microbial organisms and viral agents in the environment is far greater than previously estimated. [Nee S. (2004), "More than meets the eye","Nature", 429, 804-805.] Tools that allow the investigation of very large data sets from environmental samples using shotgun sequencing techniques in particular, such as MEGAN, are designed to sample and investigate the unknown biodiversity of environmental samples where more precise techniques with smaller, better known samples, cannot be used.

Fragments of DNA from an environmental sample, such as ocean waters or soil, are compared against databases of known DNA sequences using BLAST or another algorithmic bioinformatics tool to assemble the segments into discrete comparable sequences. MEGAN is then used to compare the resulting sequences with gene sequences from GenBank in NCBI.cite journal | last = Frias-Lopez | first = Jorge | coauthors = Yanmei Shi, Gene W. Tyson, Maureen L. Coleman, Stephan C. Schuster, Sallie W. Chisholm,band Edward F. DeLong | title = Microbial community gene expression in ocean surface waters | journal = PNAS | volume = 105 | issue = 10 | pages = 3805–3810 | publisher = National Academy of Sciences | location = United States of America | date = 2008-03-11 | url = http://www.pnas.org/cgi/reprint/0708897105v1.pdf | doi = | id = | accessdate = 2008-04-03 ] The program was designed to investigate the DNA of a mammoth recovered from the Siberian permafrost.cite journal | last = Poinar | first = Hendrik N. | authorlink = | coauthors = Carsten Schwarz, Ji Qi, Beth Shapiro, Ross D. E. MacPhee, Bernard Buigues, Alexei Tikhonov, Daniel Huson, Lynn P. Tomsho, Alexander Auch, Markus Rampp, Webb Miller, Stephan C. Schuster | title = Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA | journal = Science | volume = 331 | issue = | pages = 392–394 | publisher = American Association for the Advancement of Science | location = United States of America | date = 2007 | url = http://www.sciencemag.org/cgi/content/abstract/1123360v1?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=wooly+mammoth&searchid=1135358119618_7589&FIRSTINDEX=0&journalcode=scipaper | doi = | id = | accessdate = 2008-04-03]

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