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)

last updated Oct. 1st, 2010

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