CH505: Longitudinal within-host Env single-genome amplification...
In phraber/pixelgram: Pixel View with Accompanying Phylogram of Sequence Alignment

Description Usage Format Details Source

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.

CH505

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.
tre: The Newick-formatted phylogeny was inferred by phyml3 with HIVw and Gamma4+I.
wpi: The sample time-point at which the sequence was drawn, in weeks post-infection. Parsed from sequence names.

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.

http://hiv.lanl.gov/components/sequence/HIV/search/d_search.com?spl_pub_id=16774

http://hiv.lanl.gov/components/sequence/HIV/search/d_search.com?spl_pub_id=18294

http://ncbi.nlm.nih.gov/pubmed/23552890

http://ncbi.nlm.nih.gov/pubmed/25065977

phraber/pixelgram documentation built on May 25, 2019, 6:02 a.m.