Tools for Data Analysis – Molecular Biology

Data Analysis tools:

Given the complexity of metagenomic samples, a number of publicly available bio-informatics tools have been created.

MEGAN: (www-ab.informatik.uni-tuebingen.de/software/megan/welcome.html), a Metagenome Analyzer, allows a single scientist to analyze large data sets and group sequencing reads into taxonomic units.

The SEED database (www.theseed.org/wiki/Main_Page) is a public resource of complete and draft genome sequences to help relate sequences to metabolic function.

IMG/M (http://img.jgi.doe.gov/m) provides tools for analyzing the functional capability of microbial communities based on their metagenomic sequence, in the context of reference isolate genomes, using a variety of public functional and pathway resources.

CAMERA (http://camera.calit2.net) is a user-driven site dedicated to providing the scientific community with metagenomic data and analysis tools.

CARMA (http://www.cebitec.uni-bielefeld.de/brf/carma/carma.html) is a software pipeline for analyzing metagenomes. The Ribosomal Database Project (http://rdp.cme.msu.edu) provides tools to analyze 16S rRNA sequences.

COGs (http://www.ncbi.nlm.nih.gov/COG), NCBI’s non-redundant Clusters of Orthologs database provides phylogenetic classification of proteins encoded in complete genomes.

KEGG (http://www.genome.jp/kegg/), the Kyoto Encyclopedia of Genes and Genomes, is a reference data base for linking genomes to biological systems and environments.

Comments are closed.