Russian Metagenome Project consortium is ready for collaboration in metagenome data analysis related to human gut and any other microorganism communities. It will be our pleasure to assist you with consultation or teamwork on metagenome data analysis. Below there is a list of software packages and metagenome web services with annotations, which can be used in data analysis.
MG-RAST (http://metagenomics.nmpdr.org) – service for automatic metagenome data annotation.
IMG/M (http://img.jgi.doe.gov/m/doc/about_index.html) – integrated system for microorganisms’ genomes study, developed for metagenome research.
QIIME (http://qiime.sourceforge.net) – pipeline system for processing metagenome data. It includes software for all the study stages, starting from filtration and finishing with phylogenetic analysis and comparison of complex communities (publication).
Protein peeling. One of the possible variants to study variety of proteins in metogenomics is to identify protein functional units. Web service Protein Peeling was created by French consortium based on protein tertiary structure data. The web service searches for structural-functional protein units (http://www.dsimb.inserm.fr/dsimb_tools/peeling/ ), publication is here.
DODO. Study of complex gene data often reduces to generalization of genes at the level of ortology. For not annotated genomes a search of ortologs is required by DNA sequence. Such problem can be solved with DODO algorithm ( http://18.104.22.168:16080/dodo_web/home.htm ), publication on topic is here.