Analysis Tools

One of the main purposes of TerraGenome is to help enable the analysis of soil metagenome data. The links below will take you to existing bioinformatics resources.

  • RDP (Ribosomal Database Project): The Ribosomal Database Project (RDP) provides ribosome related data and services to the scientific community, including online data analysis and aligned and annotated Bacterial and Archaeal small-subunit 16S rRNA sequences. http://rdp.cme.msu.edu/
  • QIIME (Quantitative Insights Into Microbial Ecology): QIIME is an open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data (such as SSU rRNA) generated on a variety of platforms, but also supporting analysis of other types of data (such as shotgun metagenomic data).  http://qiime.sourceforge.net/
  • Greengenes: The greengenes web application provides access to the current and comprehensive 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading.  The data and tools presented by greengenes can assist the researcher in choosing phylogenetically specific probes, interpreting microarray results, and aligning/annotating novel sequences. http://greengenes.lbl.gov/cgi-bin/nph-index.cgi
  • MG-RAST: MG-RAST (the Metagenomics RAST) server is an automated analysis platform for metagenomes providing quantitative insights into microbial populations based on sequence data. The server provides web based upload, quality control, automated annotation and analysis for samples up to 10 GBp. Comparison between large numbers of samples is enabled via pre-computed abundance profiles.  
    http://metagenomics.anl.gov/
  • IMG/M (Integrated Microbial Genomes/Microbiome): IMG/M  provides tools for analyzing the functional capability of microbial communities based on their metagenome sequence, in the context of reference isolate genomes included from the Integrated Microbial Genomes (IMG) system. http://img.jgi.doe.gov/

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