Major class

[tibitoy]

Hi all! I am conducting an analysis where I am trying to find MGE that are near my antibiotic resistance genes (looking for MGE <10 kbp away from from my genes). As a result, I'm using the alignment.out.csv files rather than simply using the summary files. I was wondering how I can know if the gene i'm looking at is a plasmid/phage/integrative element/etc. with the alignment file? I'm working with many samples so simply searching genbank for the accession number is not possible. The alignment file gives general info (will tell you major mobileOG type) but does not tell me if something is a plasmid, for example.

[clb21565]

Hello there! Thanks for using mobileOG-db, and great question --

We have now added reproducible R code for producing element labels for mobileOGs using just the metadata (.csv) file. The resulting metadata can be accessed here. This metadata file can be used to provide classification to contigs, as in the on the mobileOG-pl usage guidance page.

Please let me know if you have any other questions.

[balaram26]

Hey i have seen the R code and the metadata, i was wondering you have mentioned that it could be incorporated into the script, but has been done already? because i saw the same metadata file is being used in the script as well. so your r code taken the alignmnet.out as input along with the meta data for classification?

[clb21565]

Hi - thanks for the question - I realize now it is kind of confusing. The R code will take in the mobileOG metadata file and produce a new metadata file that has the element classifications. But, this only needs to be done once. Then, the element classification metadata file can be merged with a diamond output file by mobileOG header name and element classifications gathered that way.

We will be addressing the element classification labels in the next major update.