User:R. Eric Collins/GenomicsTutorial/Metagenomics/Annotation

Overview
The purpose of this exercise is to become familiar with the following:

Software/Databases

 * KEGG (genomics database)
 * IMG (genomics and metagenomics database)

Get metagenomic data

 * 1) go to IMG-M
 * 2) click Microbiomes
 * 3) Find your favorite environment
 * 4) click Protein coding genes connected to KEGG pathways
 * 5) find a pathway of interest and click on the gene count
 * 6) click Select All
 * 7) click  Add Selected Genes to Cart
 * 8) under Gene Export, click FASTA Amino Acid format, then Show in Export Format
 * 9) copy and paste sequences into new text file and save to disk

Automatic Annotation

 * 1) go to KEGG Automatic Annotation Server
 * 2) under Partial Genome, click KAAS job request
 * 3) click File Upload and choose your metagenome amino acid sequence file
 * 4) fill in a Query name and your email address
 * 5) if you wish, select a set of microorganisms relevant to your environment or use the set below:
 * sty, hin, pae, bsu, aae, afu, ape, vch, par, sdn, sfr, cps, pha, pin, tcx, csa, hel, cvi, bma, pol, dvu, dvl, dde, gme, dps, gtn, dsy, psl, syw, cte, dra, tma, mmp, mac, hal, pfu, dka, sis, nmr, pub
 * 1) choose SBH as the Assignment Method
 * 2) click Compute
 * 3) check your email to find the link to obtain the results
 * 4) wait
 * 5) results!