New ways to analyze metagenomics data

Are you looking for new tools to analyze your metagenomics data? Are you using  MG-RAST, IMG/M or MEGAN for your daily metagenomics work?

JCVI is working on a user friendly alternative that you might be looking for –  a new  tool kit  for metagenomics data visualization and analysis  built using the latest web 2.0 technologies.

JCVI’s Metagenomics Reports (METAREP) is a user friendly web interface designed to help scientists browse, compare, view,  and query annotation data derived from ORFs called on metagenomics reads. It supports both functional (Gene Ontology, Enzyme Commission Classification) and browsing of taxonomic assignments. When performing a search, users can either specify fields or logical combinations of fields to flexibly filter datasets on the fly. METAREP provides lists and pie charts of top functional and taxonomic categories for browse and search results. Tools are being developed that focus on the comparative analysis of multiple datasets. The system is optimized to be user friendly and fast .

Currently, an alpha version of METAREP  is used and tested internally at JCVI. In April 2010 , we will release the beta version to a limited set of interested external users.

If you like to see the tool in action,  join us  at the DOE Genomic Science Workshop ( February 9-10, 2010) for our web and poster presentation (5:30 – 8:00 pm on each day) or sign up to become part of the beta testing process at www.jcvi.org/metarep .

4 Responses to “New ways to analyze metagenomics data”


  • I am logeswaran,pg student ,dept of biotechnology . doing my project in metagenomics:isolation of antibiotic producing gene form marine sample .I need a new method to isolation of DNA from marine water (without kit method)
    please reply immediately

  • It looks like an amazing tool for analysis of metagenomic data.

    Congratulations

  • Hi Logeswaran, according ur query what i understand is you are tring to extract DNA from some marine samples. Using that DNA as a template for 16s amplication and followed by sequencing. is that wat you wanna do?

    From marine sample there are a wide variety of bacteria which differs in their cell wall compositions as well,

    Have u checked any other publications who did DNA extraction from marine samples? For exapmle environmental shotgun sequencing of marine sargasso sea by Venter etal

    May be u will find something useful in there

    If u don’t like to use any kit, you have to filter the sample, make sure that you are using the filter that not filter ur bacteria, After filtering collect the filterate and add lysis buffer add 0.3g of acid washed glass beads and use bead beater for 2 mins and followed by Hoffmann winston DNA extraction protocol. Hope this helps

  • i got dna from marine sediment without using any kit but that DNA contianing lot of bacterial species. it is mixture of DNA .how i will know that wide veriety of species in that?

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