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.
- 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.
- 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
- 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
- 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
- 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