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

From OpenWetWare
Jump to: navigation, search

Overview

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

Concepts

Techniques

Software/Databases

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

Protocol

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!