Archive for the ‘Old blog entries’ Category

MG-RAST Version 3.1.2 released [December 20, 2011]

Tuesday, December 20th, 2011

We are pleased to announce the release of version 3.1.2 of MG-RAST with major changes to provide greater transparency to the underlying data and to make new features available on both the Overview and the Analysis page.

New Features

  • alignment visualization now available,
  • search within the metagenome analysis results for function and organism now available,
  • figure and table data download is enabled in almost all places,
  • new statistics available (hit coverage, alpha diversity, functional and taxonomic hits distribution).

Below we provide detailed descriptions of the new features and the changes.

Overview Page

The overview for a single dataset has been completely revamped to give a quick insight into the results of the MG-RAST analysis and make the analysis process and results more transparent. Additions include:

  • Pie-chart with the sequence distribution giving the breakdown of the numbers of reads annotated as RNA and protein as well as the numbers for which no annotation was found.
    MG-RAST Sequence Distribution
  • The analysis flowchart gives a quick graphical representation of the numbers of reads identified by different stages in the pipeline and will give you an idea of where the numbers used in the analyses tools come from.
    MG-RAST Analysis Flowchart
  • Pie-chart with the distribution of hits by functional category for COGs, KOs, NOGs, and SEED Subsystems. The numbers can be downloaded and the hierarchical representation can be viewed as an interactive graph using Krona.
    MG-RAST Functional Category Hits Distribution
  • Pie-chart with the distribution of hits by taxonomic domains, phyla, and order for the annotations
    MG-RAST Taxonomic Hits Distribution
  • Alpha diversity is computed for each dataset summarizing the diversity of the annotations for a dataset with a single number. The data used in the computation can be downloaded.
  • Text search for predicted functions or organisms within the analysis results of your metagenome

Analysis Page

Alignments

The BLAT hits on which the MG-RAST analyses are based can now be viewed on the new BLAT alignment page,

Interactive Krona display

The results of the hierarchical annotations can be displayed in a interactive pie-chart using Krona.

Bug Fixes

We have implemented a number of bug fixes, including:

  • projects and collection management fixes,
  • static generation of images,
  • Heatmap and PCoA IDs fixed,
  • QIIME download filtered based on selected database sources,
  • download button for heatmap data,
  • download button for PCoA values,
  • barchart titles onclick action corrected,
  • added private projects to metagenome select list,
  • fixed sharing of jobs with multiple users with single click,
  • fixed sorting of dataset IDs in PCoA.

MG-RAST v2 retired [November 21st, 2011]

Tuesday, November 8th, 2011

It is over 7 months since Version 3 was released and the time has come to retire Version 2.

This will take effect on November 21st, 2011, two weeks from this announcement, after which the server will be permanently taken down. All parts of the analyses that are dynamically produced by the website will not be reproducible after this date. This includes images for the various analyses, e.g. pie-charts, heat-maps etc. as well as the data tables and some of the downloads, if you would like a copy of any of these please download them now. The data files used for the analysis will be preserved and we can make them available to the owner of the dataset for a limited time if requested.

Please email us at mg-rast at mcs.anl.gov if you have any concerns.

Thank you for using our site and we hope that you find Version 3 a worthy successor.