lassie: lassie: Tools to select sequences that represent variation in...

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

Description

The lassie package provides methods to select sites and sequences in a protein sequence alignment obtained from longitudinal sampling, also known as LASSIE, an acronym for "longitudinal antigenic sites and sequences from intrahost evolution" or "longitudinal antigen swarm selection from intrahost evolution".

Assumptions

Start with a sequence alignment sampled serially from an infected host, which characterizes a pathogen population evolving under immune pressure. The population is related by a single common "transmitted-founder" (TF) ancestor.

Step 1. Select sites

The first phase of analysis computes TF loss per aligned site for each time-point sampled, to select sites of interest where TF loss exceeds a threshold. Sites that lose the ancestral TF amino acids are likely under positive selection and merit further investigation.

Step 2. Select sequences

The second phase selects a set of sequences with mutations among selected sites. A swarm of sequences represents diversity in the population sampled and can subsequently be used to study developing immune responses.

Tutorial

Example data are included to identify sites on the HIV-1 envelope glycoprotein, to characterize affinity maturation which leads to a broadly neutralizing antibody response. To review the tutorial, run vignette(package="lassie")

See Also

swarmtools

swarmset

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