trna-gene-hits

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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Provided by

anvi-integrate-trnaseq

Required or used by

There are no anvi’o tools that use or require this artifact directly, which means it is most likely an end-product for the user.

Description

tRNA gene hits are the matches identified between tRNA-seq seeds – the predicted tRNA transcripts from one or more tRNA-seq samples – and tRNA genes in an associated (meta)genomic sample. anvi-integrate-trnaseq stores a trna-gene-hits table in the trnaseq-contigs-db. This table not only contains information to match seeds with genes, but also the identities of unmodified nucleotides at sites of predicted modification-induced substitutions.

Here is an example with samples from a single organism. anvi-gen-contigs-database is used to make a contigs-db from the organism’s genomic sequences. tRNA-seq samples are analyzed by the trnaseq workflow. Outputs of the workflow include a trnaseq-contigs-db from anvi-merge-trnaseq and tables of consolidated data – seeds-specific-txt, seeds-non-specific-txt, and modifications-txt – from anvi-tabulate-trnaseq. tRNA seeds can be formed from de novo tRNA predictions of one or more tRNA-seq samples: hopefully most tRNAs are expressed at measurable levels in all samples. anvi-integrate-trnaseq compares seeds to tRNA genes to find confident matches and stores them in the trna-gene-hits table. It is common for a genome to have multiple copies of the same tRNA gene, resulting in a seed matched with multiple genes.

tRNA-seq samples from a metagenome differ because tRNA transcripts can arise from identical genes in multiple organisms. anvi-integrate-trnaseq can be aware of bins to restrict hits to seeds that match genes in only one bin and not genes in any other bins or unbinned contigs.

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