censored_translation

dna_str

<p>reading frame = 1 means the first bp in the string is the start of the
first codon, can pass 1, 2 or 3. For 2 and 3 the first 1 and 2 bp will be
dropped from translation respectively.</p>

reading_frame

<p>Translate a 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.</p>


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.

censored_translation: Censored Translation of a DNA string.

Description

Usage

Arguments

Details