example_barcode_data

<p>A nine line dataframe of coi5p barcode data with the following columns:
id - the unique identifier for the sample
genetic_code - the genetic code for translation of the sample (features NA for unknowns)
taxa -  a taxonomic designation associated with the sample
sequence - the DNA sequence associated with the sample
notes - notes on the sequence structure</p>

datasets


Designed for the cleaning, contextualization and assessment of cytochrome c oxidase I DNA barcode data (COI-5P, or the five prime portion of COI).
It contains functions for placing COI-5P barcode sequences into a common reading frame, translating DNA sequences to amino acids and for assessing
the likelihood that a given barcode sequence includes an insertion or deletion error. The error assessment relies on the comparison of input sequences
against nucleotide and amino acid profile hidden Markov models (for details see Durbin et al. 1998, ISBN: 9780521629713) trained on a taxonomically
diverse set of reference sequences. The functions are provided as a complete pipeline and are also available individually for efficient and targeted
analysis of barcode data.

Cameron Nugent

coil

Contextualization and Evaluation of COI-5P Barcode Data

example_barcode_data function

<p>An object of class <code>data.frame</code> with 9 rows and 5 columns.</p>

example_barcode_data: Example barcode data.

Description

Usage

Arguments

Format