censored_translation

Translate a DNA sequence using the censored translation table.
This translates codons for which the amino acids are 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.

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

censored_translation function

<dl><dt>dna_str</dt>
<dd>The DNA string to be translated.</dd>
<dt>reading_frame</dt>
<dd>Set the reading frame of the sequence. reading_frame = 1 (default)
means the first bp in the string is the start of the first codon, can pass: 1, 2, or 3.
i.e. reading_frame = 2 indicates that the second bp in the string is the start of the first codon.</dd></dl>

Arguments

Censored Translation of a DNA string. — censored_translation

<dl>

<dt>dna_str</dt>
<dd>The DNA string to be translated.</dd>


<dt>reading_frame</dt>
<dd>Set the reading frame of the sequence. reading_frame = 1 (default)
means the first bp in the string is the start of the first codon, can pass: 1, 2, or 3.
i.e. reading_frame = 2 indicates that the second bp in the string is the start of the first codon.</dd>

</dl>

censored_translation: Censored Translation of a DNA string.

Description

Usage

Arguments

Examples