No further updates to the MicrobesOnline database are planned, although minor improvements to the web site did occur in 2016. New genomes were last loaded in late 2011.

March 2011 release notes

• Code update only
• Links to SEED (example)
• View microarray summary by organism

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

• Downloadable species tree available with names (see download links from the main species tree page)
• ECs, KEGG map titles and compounds now searchable on KEGG maps (see the search box on the metabolism map)
• HAMAP families (from InterProScan) now included
• Microarray data analysis for fungi: heatmaps, gene-gene expression correlations, and gene expression profile searches.
• Microarray experiments from M3D (examples) and Gasch (examples)

March 2010 release notes

• Almost 100 fungal and selected eukaryotic genomes from the Fungal Genome Institute and the DOE Joint Genome Institute
• Microarray data for fungi available in our microarray data section
• Gene trees and species tree are now computed with our maximum likelihood tool, FastTree 2
• HMM domains using HMMer 3, including HMMer 3 models from PFam
• Predicted gene regulation from RegPrecise (example)
• Protein-protein interaction data (example gene) (example genome)
• Ease of use improvements:
  • New home page with examples to MicrobesOnline functionality
  • Genome selector now accepts "All cellular organisms" as a search term
  • Specify genomic coordinates to view in the genome browser (example)

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)

MicrobesOnline Home Page