Q(uestion): Hi, When will the record of this webinar be available online?
A(answer): Webinar recording(s) will be made available after the last one on June 16th, 2020
Q : Is there a maximum number of genes that IMG can save in a cart/workspace?
A : There is a limit to the amount of data in Workspace. It is 5Gb per user, the combined size of all sets and files being generated, like fasta files for export. The limit on the carts is 20,000 (20,000 genomes, 20,000 genes, 20,000 scaffolds, 20,000 functions). Note that you may have to change your preferences by going to MyIMG -> Preferences to increase the display limits to the maximum number of objects.
Q : Can you share the link for the public query?
A: Here it is: https://img.jgi.doe.gov/cgi-bin/mer/main.cgi?section=Workspace&page=public_genome_search_history
And you can view the Advanced Genome Search Webinar for more information re. genome search: https://bit.ly/IMGwebinar20GenomeSearch
Q : Why is only this module selected and not the others?
A : It’s relevant to the demo biological example that was outlined in the slides. She is interested in seeing if N2 fixation and nodulation functions are present across all Bradyrhizobia.
Q : I missed what the difference between function vs genomes and genomes vs function was.
A : Selecting one or the other will determine rows vs columns orientation. Function (rows) vs genomes (columns) or vice versa
Q : Is the search based on annotations metadata or sequences?
A : It’s based on sequence annotations. Protein CDS are searched against (for example) Pfam, COG, or Kegg Orthology databases – you could do the same search using other annotations as well. You are then querying the results of these annotations using IDs or search terms.
Q : Is it possible to not find a gene due to outdated annotation from several years ago?
A : Yes, it is a possibility. Some very old genomes in IMG were annotated using an older pipeline, those genomes do not undergo structural re-annotation (that is, there are no updates of ORF finding and CDS calling). However, there are updates of functional annotations of existing CDS – even for older genomes (isolates only) – Pfam, Tigrfam, COG, KO, etc assignments are updated with the latest versions of these databases.
Q : And the other explanation might be due to the horizontal transfer of those genes which do not share the characteristics of the rest of the genome
A : Yes, agree. Horizontally transferred regions would be also missed by the binning process, and so will be other regions with deviant oligonucleotide composition, like ribosomal operons, if they are found on a separate contig, and not assembled with a large fragment of core genome.