Microbial 'omics

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hmm-hits [artifact]

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A CONCEPT-type anvi’o artifact. This artifact is typically generated, used, and/or exported by anvi’o (and not provided by the user)..

Back to the main page of anvi’o programs and artifacts.

Provided by

anvi-run-hmms anvi-scan-trnas

Required or used by

anvi-delete-hmms anvi-get-sequences-for-hmm-hits 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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