MEGAN
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| MEGAN | |
|---|---|
| Developed by | Daniel Huson et al. |
| Latest release | 2beta8 / 2008 |
| OS | Windows, Linux, Mac OS X |
| 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.[1]
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.[2] 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.[3] The program was designed to investigate the DNA of a mammoth recovered from the Siberian permafrost.[4]
[edit] References
- ^ Huson, H.; A. Auch, Ji Qi, and S. C. Schuster (2007). "MEGAN Analysis of Metagenomic Data". Genome Research 17: 377–386. Woodbury, New York: Cold Spring Harbor Laboratory Press.
- ^ Nee S. (2004), "More than meets the eye",Nature, 429, 804-805.
- ^ Frias-Lopez, Jorge; Yanmei Shi, Gene W. Tyson, Maureen L. Coleman, Stephan C. Schuster, Sallie W. Chisholm,band Edward F. DeLong (2008-03-11). "Microbial community gene expression in ocean surface waters". PNAS 105 (10): 3805–3810. United States of America: National Academy of Sciences.
- ^ Poinar, Hendrik N.; 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 (2007). "Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA". Science 331: 392–394. United States of America: American Association for the Advancement of Science.
