Q(uestion): Do the viruses include prophage that are integrated into bacterial genomes?
A(nswer): Not right now. We’re working on the new version of IMG-VR, which will include prophage
Q: Is this webinar being recorded for future reference?
A: Yes, it is being recorded and the recording will be posted. You'll get the link.
Q: Symbionts associated with marine invertebrates would be Host-associated or Environmental?
A: These would be host-associated. We know, it may be confusing. One of the hardest cases that we’ve seen are so-called fungal gardens – fungi cultivated by leaf cutter ants on shredded leaves. It is sort of host-associated, but also somewhat engineered 🙂
Q: Is it mandatory to classify our sample in all levels to submit it to IMG?
A: No. We ask you to classify the sample at the broadest level of environmental category (host-
Q: Is it possible to search for Conserved Domains using cdd name?
A: No, IMG doesn’t have CDD database, only some of the components (COGs, Pfams, TIGRfams, SMART).
Q: Is there a way to search a particular gene in entire bacterial genome database?
A: It depends on the definition of a "particular gene". If you have the sequence, you can run
BLAST against all IMG isolates.
Q: I do the same search, I get a different (smaller) number of hits.
A: Rekha is what we call a “superuser,” meaning that she has access to a bunch of private
genomes to which you don’t have access. It is expected that you see smaller number of hits.
Q: Blast search option will be covered today’s webninar?
A: No, it will be one of the webinars that we’re planning. We’ve settled on the first 4, and are
asking for the feedback as to the additional topics that we need to cover. IMG similarity
searches is one of the possible topics.
Q: Is searching for PFAM fold an option in the advanced search builder? I can’t seem to see it..
A: Search for Pfams is in the Gene Search. You can search by Pfam id, name, or construct a
complex query with Advanced Search.
Q: What is the difference between IMG and genome portal?
A: JGI Genome Portal is the place where you go to download the data in bulk. IMG provides
tools for data analysis and some (not bulk) download. It may not be obvious with Genome
Search, but will be more clear with additional tools.
Q: Would it be possible to do this same type of search for a particular bacterial species with a
set of Metagenomics that I have saved in my Workspace?
A: A short answer is "not through Advanced Genome Search". A long answer is that IMG has
several options to search for a particular species in metagenomic data. We're soliciting
feedback for future webinar topics, this can be one of them.
Q: For analysis with metagenome data, I need a known sequence of a gene? It is the first time
that I am going to carry out this type of study
A: It depends on how you want to analyze the metagenome data. If you want to find homologs
of a particular gene in metagenomic data, then you need either its sequence or its affiliation
with some protein family, like Pfam.
Q: Are the genomes in GOLD or submitted to IMG also deposited in GenBank?
A: No. You need to do your own GenBank submissions. If the genomes are JGI sequenced, we do submit. But for all externally sequenced genomes you annotate in IMG, user do their own GenBank submissions. IMG (and GOLD) have 3 types of genomes: JGI-generated; private submissions not sequenced by the JGI; public genomes downloaded from GenBank. The third category is in GenBank. JGI-generated genomes eventually are submitted to GenBank, with the
exception of single-cell genomes and metagenome-assembled genomes. Private submissions may or may not go to GenBank.
Q: Can we keep the annotation from JGI when submit to GenBank? So we don’t need to do a re-annotation via GenBank
A: Yes, you can use the JGI annotation to submit the genome to GenBank or reannotate at GenBank. The reason why we don't provide this service to external submitters is because we never or almost never have the complete metadata in order to generate structured comment for the submission. However, JGI-generated gff files generally pass GenBank validation, so you can use them for submission.
Q: How to analyze hypothetical proteins more elaborately? What is the difference between
draft and permanent draft genome?
A: WRT hypothetical proteins, we can try to address this in on of the future webinars. WRT
draft vs permanent draft, “draft” in general means that people may continue sequencing efforts
in order to improve the assembly. “Permanent draft” means that no more sequencing is being
done. You will find definitions for these and other terms used at the following help pages on
GOLD https://gold.jgi.doe.gov/help -> GOLD Terminology
Q: Hi, I have a question about the special symbols are acceptable in the searches. For example I
learned today to use “<=” symbol for less than or equal. Are there other useful symbols?
A: Search Builder accepts ranges expressed as “x to y.” In Results you can filter tables using Perl
regular expressions. We’ll post some advanced examples to show how exactly these can be
Q: I cannot follow sometimes. Can we get the recorded video somewhere? That would great
help to review what we discussion today.
A: Yes, the webinar is being recorded and will be posted. You will get the link.
Q: I am really interested in the workshop, but I am not pretty sure whether I would be able to
participate due to the vise issue. Can I get refund if I am not able to attend?
A: Yes, you will be fully refunded for registration if you cannot attend.