Microbial 'omics


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trnaseq-db [artifact]

Table of Contents

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)..

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Provided by

anvi-trnaseq

Required or used by

anvi-merge-trnaseq

Description

A tRNA-seq database contains information on tRNA sequences predicted from a single tRNA-seq sample.

This database is the key output of anvi-trnaseq. That program predicts which reads are tRNA through structural profiling, clusters tRNA reads into discrete biological sequences, and predicts the positions of nucleotide modifications.

The series of steps implemented in anvi-trnaseq sequentially adds the following information to the database.

  • Unique sequences predicted to be tRNA, including read counts
  • Primary sequence and secondary structural features (stems and loops) predicted in each profiled tRNA
  • Unconserved nucleotides in the primary sequence that differ from expectation
  • Unpaired nucleotides in the stems
  • “Trimmed” tRNA sequences, formed from unique sequences only differing by 3’ nucleotides of the CCA acceptor region and 5’ nucleotides beyond the acceptor stem
  • “Normalized” tRNA sequences, formed by dereplicating trimmed tRNA sequences that are 3’ fragments from incomplete reverse transcription and by mapping biological 5’ and interior tRNA fragments
  • Potentially modified tRNA sequences, formed by clustering normalized tRNA sequences and retaining those clusters that differ by 3-4 nucleotides at aligned positions

This database is the key input to anvi-merge-trnaseq, which takes one or more databases comprising the samples in an experiment and generates a trnaseq-contigs-db of tRNA seed sequences and trnaseq-profile-dbs. These tRNA-seq variant contigs and profile databases can then be manipulated and displayed in anvi’o like normal contigs-dbs and profile-dbs.

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