translate_codon

Translate a codon of DNA sequence using the censored translation table.
this translates codons for which the amino acids is unambiguous across
mitochondrial genetic codes across the animal kingdom and does not
translate those for which the amino acid varies,
but rather outputs a ? in the string.

internal

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 (PHMMs) (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

translate_codon function

<dl><dt>codon</dt>
<dd>a three letter DNA string.</dd></dl>

Arguments

Censored Translation of a codon. — translate_codon

<dl>

<dt>codon</dt>
<dd>a three letter DNA string.</dd>

</dl>

translate_codon: Censored Translation of a codon.

Description

Usage

Arguments

Details