I am currently screening for antibiotic resistance in strains of Staphylococcus aureus, the strains that I am using are already assembled, sequenced and annotated. I have used ResFinder to screen the strains and I want to confirm my results with another database. I have decided to use ARG-Annot. I have downloaded a nucleotide database but I am missing a protein database, and I am unable to find one. If anyone has any suggestions to how I can properly set up ARG-Annot or if there is a better database I should be using?
Thank you.
Preferably select sequences that fit your research field and have already been published. There are several databases in your field of research:
***First of all, "uniprot.org" is recommended. Which is an extraordinary database concerning Protein Sequence, Expression, Domains detail, and functional information: Uniprot.org
***ExPASy is the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools including proteomics, genomics, phylogeny, transcriptomics, etc.: Expasy.org
**The Comprehensive Antibiotic Resistance Database (CARD): card.mcmaster.ca
**Finding antibiotic-resistant genes: http://sepsis-omics.github.io/tutorials/modules/abricate/
**AMRFinderPlus: https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder/
**Finding AMR data in PATRIC. Examining Antimicrobial Resistance (AMR): https://docs.patricbrc.org/tutorial/amr/amr.html
*The Pfam database of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). This site is a subset of the EMBL-EBI database: pfam.xfam.org
*This site is more useful when you study metabolic pathways: Genome.jp
*The DNA Data Bank of Japan Ddbj.nig.ac.jp
can try either one of the below:
AMRFinderPlus (NCBI): https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder/
Resistance Gene Identifier (RGI) (CARD): (https://card.mcmaster.ca/analyze/rgi)
There will be some overlapped genes with the above and ResFinder.
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