R/CH505.R

In phraber/pixelgram: Pixel View with Accompanying Phylogram of Sequence Alignment

#' Longitudinal within-host Env single-genome amplification alignment.
#'
#' An alignment of 384 + 2 full-length HIV-1 envelope glycoprotein (env) gp160 
#' amino-acid sequences sampled from 4 (w004) through 160 (w160) weeks 
#' post-infection.  The study participant identifier is 703010505, aka CH505.
#'
#' For the record, 397 sequences from CH505 are available in this sample 
#' interval. Thirteen sequences have been excluded from this alignment, 
#' two with unique long insertions relative to the TF (w009.33.KM284795 and 
#' w136.B1.KC247403) and eleven with a shared 321-nt deletion, which most 
#' likely results in an inviable Env.  The two sequences with long insertions
#' explain why so many gapped columns in the alignment are unoccupied, i.e. 
#' the gaps are place-holders for the long insertions.  It is unclear whether 
#' the shared deletions result from sequencing or replication error.
#'
#' @format
#' \describe{
#'   \item{aas}{Sequence names contain up to three dot-separated fields, 
#' indicating weeks post-infection, amplicon identifier, and database 
#' accession number.  Two additional sequences are the HXB2 reference for 
#' numbering positions and the inferred transmitted-founder virus, which 
#' matches multiple Envs.  In the sequence text, asparagines in potential 
#' N-linked glycosylation sites are indicated as "O".  Gap characters ("-") 
#' are inserted to maintain aligned sites.  "Z" indicates a stop codon.  
#' "X" indicates an incomplete or ambiguous codon.}
#'   \item{tre}{The Newick-formatted phylogeny was inferred by phyml3 with HIVw
#' and Gamma4+I.}
#'   \item{wpi}{The sample time-point at which the sequence was drawn, in weeks post-infection.  Parsed from sequence names.}
#' }
#' @source \url{http://hiv.lanl.gov/components/sequence/HIV/search/d_search.com?spl_pub_id=16774}
#' @source \url{http://hiv.lanl.gov/components/sequence/HIV/search/d_search.com?spl_pub_id=18294}
#' @source \url{http://ncbi.nlm.nih.gov/pubmed/23552890}
#' @source \url{http://ncbi.nlm.nih.gov/pubmed/25065977}
"CH505"