Arjun Prasad

Hi Torsten, You make a good point. Now that there are several different makeblastdb commands (nucleotide and protein) it would be nice to enable just running that portion of the...

So it occurred to me that I have the same problem. I make modifications to the database, and I use a Makefile. I know it's not as good as a...

Hi @conchaeloko, I haven't used it to screen phage specifically, but assuming you're screening assembled sequence for the phage AMRFinderPlus should identify bacterial AMR genes included in that sequence. Note...

Hi, You're right the AMR_DNA-*.tab files don't contain all the point mutations, only those found on DNA sequences (e.g., 16S or promoter mutations). The other mutations are screened using protein...

@kwonsoobin I just happened to read this again, and I thought I'd mention that if you're interested in nucleotide sequences behind the point mutations, you can download the nucleotide sequences...

Hi Irene, There are a few points you bring up. I'll discuss one-by-one: > it would be nice if a matrix 1/0 representing presence/absence for each gene is generated. We...

Hi Irene, Thanks for posting the examples. Now I understand what you're talking about. We do ourselves transform the AMRFinderPlus output to a format similar to what you are describing...

Hi Eric, Thanks for writing, and yes the database location behavior is perhaps not ideal. We spent some time discussing alternatives so I'm glad to hear your opinions. First off...

Hi Michael, Thanks for your kind words. To suggest new mutations and/or genes please email us at [email protected]. We ask that you include the mutation, reference accession, resistances conferred, and...

Thanks for your suggestion. I'm not actually sure why we aren't using relative links for that. I think that an earlier version of the software did (or maybe what I'm...