CH505: Within-host longitudinal Env single-genome amplification...

In phraber/lassie: Tools to select sites and sequences that represent variation in a longitudinally sampled protein alignment

Description

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.

Usage

CH505

Format

sequence name

Up to three dot-separated fields, indicating time post-infection, in weeks, the amplicon identifier, and the database accession number. Two additional sequences are the HXB2 reference for numbering positions and the inferred transmitted-founder virus, which matches multiple Envs.

sequence text

Asparagines 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.

Details

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.

Source

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/lassie documentation built on May 25, 2019, 6:01 a.m.