set_frame

<p>Uses the path of the ntPHMM to locate the first contiguous
set of 5 matching base pairs (5 sequential 1s) for both the
front and the back of the sequence. Sequence information outside of this
first set of matches is trimmed (low probability of being true barcode sequence).</p>

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

set_frame: Take an input sequence and get it into the reading frame.

Description

Usage

Arguments