meta.microbesonline.org

metaMicrobesOnline - A website for browsing and comparing microbial metagenomes

MetaMicrobesOnline offers somewhat different functionality from isolate-only MicrobesOnline. Please alert us to any issues at help@microbesonline.org. Or select from Favorites:. MG: Compost, Thermophilic SG Enrichment SG0.5Z960 (454 Illumina assembly). MG: Compost, Thermophilic SG Enrichment SG0.5JP960 (454 Illumina assembly). MG: Air, Singapore Air Sample 1. MG: Air, Singapore Air Sample 2. MG: Animal Associated, Bovine, Gut, Cow rumen, Fiber Adherent - Steer 64. MG: Animal Associated, Human, Gut, Faece...

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metaMicrobesOnline - A website for browsing and comparing microbial metagenomes | meta.microbesonline.org Reviews

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MetaMicrobesOnline offers somewhat different functionality from isolate-only MicrobesOnline. Please alert us to any issues at help@microbesonline.org. Or select from Favorites:. MG: Compost, Thermophilic SG Enrichment SG0.5Z960 (454 Illumina assembly). MG: Compost, Thermophilic SG Enrichment SG0.5JP960 (454 Illumina assembly). MG: Air, Singapore Air Sample 1. MG: Air, Singapore Air Sample 2. MG: Animal Associated, Bovine, Gut, Cow rumen, Fiber Adherent - Steer 64. MG: Animal Associated, Human, Gut, Faece...

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10 gene info

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metaMicrobesOnline - A website for browsing and comparing microbial metagenomes | meta.microbesonline.org Reviews

https://meta.microbesonline.org

MetaMicrobesOnline offers somewhat different functionality from isolate-only MicrobesOnline. Please alert us to any issues at help@microbesonline.org. Or select from Favorites:. MG: Compost, Thermophilic SG Enrichment SG0.5Z960 (454 Illumina assembly). MG: Compost, Thermophilic SG Enrichment SG0.5JP960 (454 Illumina assembly). MG: Air, Singapore Air Sample 1. MG: Air, Singapore Air Sample 2. MG: Animal Associated, Bovine, Gut, Cow rumen, Fiber Adherent - Steer 64. MG: Animal Associated, Human, Gut, Faece...

INTERNAL PAGES

meta.microbesonline.org

1

MicrobesOnline Release Notes

http://meta.microbesonline.org/releasenotes.html

October 2010 Metagenomics release notes. Is released, with metagenomic data sets (120 ecological, 32 organismal) integrated with MicrobesOnline isolate genomes from the July 2010. MetaMicrobesOnline offers gene and domain family assignment for metagenomes. Currently the provided gene and domain families are COG. Genome-context browsing is available, combining environmental contigs and isolate genomes. Phylogenetic analysis using FastTree. Phylogenetic analysis showing domain combinations is also available.

2

FastTree 2.1: Approximately-Maximum-Likelihood Trees for Large Alignments

http://meta.microbesonline.org/fasttree

Also see Fast Tree-Comparison Tools. FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. For large alignments, FastTree is 100-1,000 times faster than PhyML 3.0. FastTree is open-source software - you can download the code below. GTR) models of nucleotide evolution and the JTT ( Jones-Taylor-Thornton 1992. These papers describe Fas...

3

Publications

http://meta.microbesonline.org/pubs.html

To cite this website, please use this paper. Price, M.N. et. al. FastTree 2 - Approximately Maximum-Likelihood Trees for Large Alignments. Dehal, P.S. et. al. MicrobesOnline: an integrated portal for comparative and functional genomics. D Chivian, E. L. Brodie, E. J. Alm, et. al. Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth. Molecular Biology and Evolution. 2007, 3(9): e175. MN Price, A.P. Arkin, E.J. Alm. The Life-cycle of Operons. AB Leaphart et al. Transcriptome prof...

4

MicrobesOnline for Programmers

http://meta.microbesonline.org/programmers.html

Tools and Downloads for Programmers. How to connect to pub.microbesonline.org. How to download auxilliary data: BLAST and FastBLAST databases. Obtaining our source code. Overview of the perl modules. Installing your own web server. Linking to the MicrobesOnline genome browser. This page gives technical advice on how to programmatically obtain data from the MicrobesOnline data. Please see the tutorial. For background on MicrobesOnline and on the data it contains. SELECT DISTINCT Taxonomy.taxonomyId, T...

5

FastHMM and FastBLAST: Tools for Analyzing Large Protein Sequence Databases

http://meta.microbesonline.org/fasthmm

FastHMM and FastBLAST: Tools for Analyzing Large Protein Sequence Databases. Read the paper: FastBLAST: Homology Relationships for Millions of Proteins. Downloading and Installing FastHMM/FastBLAST. FastHMM's Performance and Sensitivity. Running FastHMM on a Single Computer. Running FastHMM on a Cluster. Required Input for FastBLAST. Running the First Stage of FastBLAST. Running the Second Stage of FastBLAST. FastBLAST Merge: Adding Sequences to a FastBLAST Database. Tarball for the code. To find instanc...

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microbesonline.org

MicrobesOnline Release Notes

http://www.microbesonline.org/releasenotes.html

March 2011 release notes. Links to SEED ( example. View microarray summary by organism. October 2010 Metagenomics release notes. Is released, with metagenomic data sets (120 ecological, 32 organismal) integrated with MicrobesOnline isolate genomes from the July 2010. MetaMicrobesOnline offers gene and domain family assignment for metagenomes. Currently the provided gene and domain families are COG. Genome-context browsing is available, combining environmental contigs and isolate genomes. Microarray data ...

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metaMicrobesOnline - A website for browsing and comparing microbial metagenomes

MetaMicrobesOnline offers somewhat different functionality from isolate-only MicrobesOnline. Please alert us to any issues at help@microbesonline.org. Or select from Favorites:. MG: Compost, Thermophilic SG Enrichment SG0.5Z960 (454 Illumina assembly). MG: Compost, Thermophilic SG Enrichment SG0.5JP960 (454 Illumina assembly). MG: Air, Singapore Air Sample 1. MG: Air, Singapore Air Sample 2. MG: Animal Associated, Bovine, Gut, Cow rumen, Fiber Adherent - Steer 64. MG: Animal Associated, Human, Gut, Faece...

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