How to find old metagenome gene oids in the new IMG/M or IMG/MER

[Ken Chu]

IMG has remapped old metagenomes gene oids to a new format. For example, old gene oid 2004206642 has been replaced with a new gene oid orf1_0004_16. In most cases it will be the locus tag.

Bookmarked old metagenome gene detail page

For old metagenome gene details urls / bookmarks will be redirected to the new gene detail page with a new url.

e.g. url

http://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=2004206642

will be redirected to page

http://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=MetaGeneDetail&page=metaGeneDetail&data_type=assembled&taxon_oid=2004178001&gene_oid=orf1_0004_16

How to do a Gene Search

You can do a gene search for old metagenome gene oids.

Steps.

1. On the homepage of IMG/M do a quick genome search for the metagenome of interest e.g. genome id 2004178001 and add the resulting genome to the genome cart. This step is used to speed up gene search. 
2. In the genome search result page. Select the genome and press "Add Selected to Genome Cart" button.
3. In the menu select Find Genes -> Gene Search.
4. On the Gene Search page enter a keyword: 2004206642, 2004206643, 2004206644, 2004206645 (these are old gene oids). In the filters pick list select "IMG Gene ID (list, case-sensitive for MER-FS)*"
5. Make sure you select the genome in the Genome Filter genome list.
6. Press Go button
7. You should see a resulting table with 4 genes. The new gene oids are orf1_0004_16, orf2_0004_16, orf3_0004_16, orf4_0004_16.

Screenshots of the above 7 steps.

 Quick Genome search.

 Add Genome Search results to Genome Cart.

 Go to Gene Search Page

Search for old gene oids

 Results of gene search