MicrobesOnline Release Notes

October 2010 Metagenomics release notes

  • metaMicrobesOnline is released, with metagenomic data sets (120 ecological, 32 organismal) integrated with MicrobesOnline isolate genomes from the July 2010 isolate-only MicrobesOnline release.
  • metaMicrobesOnline offers gene and domain family assignment for metagenomes. Currently the provided gene and domain families are COG, Pfam, and TIGRFAM.
  • Genome-context browsing is available, combining environmental contigs and isolate genomes.
  • Phylogenetic analysis using FastTree trees for all genes is available, combining genes from metagenomes and isolates for gene and domain families from COG, Pfam, and TIGRFAM, a first-of-its-kind resource.
  • Phylogenetic analysis showing domain combinations is also available.
  • Gene calls are from IMG-M and MG-RAST. Gene and domain family assignments are done using the MicrobesOnline pipeline.

July 2010 release notes

March 2010 release notes

June 2009 release notes

  • Hundreds of new bacterial and archaeal genomes from RefSeq release 34
  • Fungal genomes from RefSeq now available
  • Microarray data sparklines for genes, experiments, and gene expression profile search results
  • Microarray Data
    • Over 1000 E.coli (on our main site) and S.cerevisiae (on the fungi beta site) microarray experiments uploaded from M3D
    • Microarray data for fungi is not yet available; please see our beta site
    • The 173 Gasch et al S.cerevisiae microarray experiments have been uploaded
    • Instructions for the formatting of your microarray data so that we can host it on MicrobesOnline are now available here.
  • Better performance on new hardware
  • View detailed compound information and presence/absense in user-selected genomes
  • Find genes by phyletic pattern
  • View sequence alignments and paired alignments and trees using JEvTrace.
  • Tree and ortholog browsers now support introns
  • Improved, faster genome selector using AJAX

March 2009 release notes

  • Improved keyword searching, using KinoSearch
  • Use FastTree 1.0 for improved topological accuracy in prebuilt gene trees
  • Tree-based ortholog assignments
  • Operon predictions based on new ortholog assignments and microarray data (if available)
  • Phylogenetic profile viewer for families, orthologs, and enzyme classifications (see example)
  • New 23S (see example) and 5S (see example) gene trees
  • View downstream and upstream sequences for genes in a gene cart
  • View conservation of hits to a regulatory motif
  • Microarray data now links to the MeV viewer applet (uses Java WebStart)
  • Experiment-experiment correlations for sets of microarray experiments
  • Download user-selected microarray experiment datasets
  • Microarray profile searches available for all organisms with microarray data

September 2008 release notes

  • Updated tree-building tools: FastTree (fast and accurate) and PhyML aLRT (most accurate, and gives support values)
  • Pre-computed gene trees are more accurate and have support values for large trees (FastTree 0.9 instead of QuickTree)
  • Tree browser uses orthologs to quickly guess which tree is the best to show
  • Correlation heatmaps show how correlated the expression of genes in an operon or in a gene cart are

October 2007 release notes

  • Over 400 new genomes
  • Thousands of new viruses and plasmids
  • New microarray data and interface (for some genomes)
    • Over 150 E.coli experiments imported from the Many Microbes Microarray Database
    • Compare expression patterns of selected genes
    • Dynamic search for other genes with similar expression
  • Fast sequence search (based on FastBLAST)
  • FastHMM, and a gene-domain alignment viewer
  • Links to genes with known regulation at RegTransBase
  • Links to proteins with solved structures at PDB
  • An improved species tree, including comparisons of alternate species trees
  • Trees for more gene families, and UI improvements to the gene tree browser
  • CRISPR sites and CRISPR spacer sites (for some genomes)

last updated Oct. 1st, 2010

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