A CONCEPT-type anvi’o artifact. This artifact is typically generated, used, and/or exported by anvi’o (and not provided by the user)..
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anvi-run-hmms anvi-scan-trnas anvi-script-filter-hmm-hits-table
anvi-delete-hmms anvi-get-sequences-for-hmm-hits anvi-run-scg-taxonomy anvi-script-filter-hmm-hits-table anvi-script-gen-hmm-hits-matrix-across-genomes anvi-script-get-hmm-hits-per-gene-call
The search results for an hmm-source in a contigs-db. Essentially, this is the part of a contigs-db that handles the HMM data. In anvi’o, this is usually functional annotations, such as identifying specfic ribosomal RNAs, various single-copy core genes, and transfer RNAs, though the user can also define their own HMM sources.
Upon creation, a contigs-db will not contain any HMM results. In order to populate it, users can run anvi-run-hmms using any hmm-source. The program anvi-scan-trnas also populates a contigs-db’s hmm-hits with potential tranfer RNA hits.
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