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AMRFinderPlus v3.12.8

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@evolarjun evolarjun released this 05 Feb 16:38
amrfinder_v3.12.8
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Learn about vigilant mode.

AMRFinderPlus v3.12.8 includes a new database format version. Because this version is incompatible with AMRFinderPlus databases from previous versions, amrfinder -u must be run once the software update is installed to get the latest version of the database.

This update includes the changes:

  • Reference proteins now have stop codons. Input proteins that are not terminated with a ‘’ character are assumed to have a ‘’ at the end.
  • Extended proteins are no longer “EXACT” hits, so the protein names will be that of the parent node for alleles.
  • If a protein is hit by blast and the Blast Rule is violated, the Blast Rule of the parent family is checked, etc.
  • --annotation_format prodigal input format added

This means that Previously extended hits that were 100% identical to, but longer than proteins in the database were called with the method "EXACTP" and now they are called "BLASTP". Blast results will still indicate that 100% of the database reference was covered at 100% identity, and you should still see that the "Target length" is longer than the "Reference sequence length".

  1. Extended hits to allele sequences that were previously called EXACTP already had the element symbol was one node up the hierarchy (i.e. the gene symbol, not the allele symbol) the "Sequence name" was that of the ALLELE reference, and thus inconsistent with the element symbol assigned. This has been changed. Again, this does not affect previous "Element symbol" calls.

  2. In combined protein + nucleotide runs of AMRFinderPlus extended protein sequences with exact matches in the database were ignored and the nucleotide match was taken resulting in an EXACTX match with no protein accession provided. Now the protein match with method BLASTP will be reported.

To reiterate, gene symbols should not change. Sequence names will only change if the query is an extended version of a protein 100% identical and completely covering an allele in the database.

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