trnaseq-contigs-db

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

🔙 To the main page of anvi’o programs and artifacts.

Provided by

anvi-merge-trnaseq

Required or used by

anvi-plot-trnaseq anvi-tabulate-trnaseq

Description

A tRNA-seq contigs database is a contigs-db variant containing information on tRNA transcripts identified from tRNA-seq experiments.

This database is created by the program, anvi-merge-trnaseq, which is part of the trnaseq-workflow. This program also creates trnaseq-profile-dbs. anvi-run-trna-taxonomy populates the tRNA-seq contigs database with taxonomic annotations.

This database functions in a manner equivalent to the normal metagenomic-style contigs database. As normal contigs databases are associated with a normal profile-db containing coverage-related data, tRNA-seq contigs databases are associated with trnaseq-profile-dbs. The name can be misleading: tRNA-seq contigs databases do not contain information on assembled contigs as such. Rather, the fundamental type of sequence reconstructed from a tRNA-seq experiment is a tRNA seed, representing a mature tRNA sequence (minus the 3’-CCA acceptor) found in one or more samples in the experiment. tRNA seeds are not predicted by assembly at all, but by the specialized software of anvi-trnaseq and anvi-merge-trnaseq.

A variety of information on tRNA seeds is contained in a tRNA-seq contigs database, including structural profiles, taxonomic annotations, and user-defined bins.

Uses

Tabulation of tRNA-seq data by anvi-tabulate-trnaseq requires a tRNA-seq contigs database and trnaseq-profile-db.

Interactive visualization of tRNA-seq datasets in anvi-interactive requires this database and a trnaseq-profile-db.

Visualization of grouped seeds by anvi-plot-trnaseq requires this database in addition to files produced by anvi-tabulate-trnaseq.

Edit this file to update this information.