basics.Rmd

## LASSIE selects sites and sequences from a protein sequence alignment obtained from longitudinal sampling, to represent variation induced by putative immune selection.

Please read [this] (http://mdpi.com/1999-4915/7/10/2881) paper for the whole story.

### 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.  This is generally the first
sequence in the alignment.  However, the HXB2 reference sequence can
precede the TF sequence, used only to standardize numbering of
alignment columns.

Sequence names are assumed to contain information to identify when
each was sampled.  By default, this is taken to be the first
dot-delimited field.  However, different field positions and field
separators can be specified, if necessary, via "Advanced Options".
Units for the sample timepoints are arbitrary, but assumed to be
consistent throughout.  That is, mixing days and weeks post-infection
(for example) is currently unsupported.  Also, sample dates will
probably not get sorted correctly, unless you use some clear format
like YYYYMMDD or YYYY/MM/DD.  If you label sample timepoints this way,
use a different delimiter to distinguish the field that contains the
date from the date fields themselves.  For example
`ptid_YYYY-MM-DD_then-clone-or-well-id` will work, but
`ptid.YYYY.MM.DD.then.clone.or.well.id` will not work, because you
will be unable to extract and sort all fields used for date values.

### 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.  

### Citation


If you use the CH505 example data in publication, please cite
Liao et al., 2013 (http://ncbi.nlm.nih.gov/pubmed/23552890) and
Gao et al., 2014 (http://ncbi.nlm.nih.gov/pubmed/25065977).

To cite `lassie`, please use:

```{r eval=FALSE}
Hraber P, Korber B, Wagh K, Giorgi EE, Bhattacharya T, et al.  Longitudinal antigenic sequences and sites from intra-host evolution (LASSIE) identifies immune-selected HIV variants.  Viruses 7(10): 5443-5475, 2015.
```

Thank you!

BibTeX entry for LaTeX

```{r eval=FALSE}
@Article{,
  title = {Longitudinal Antigenic Sequences and Sites from Intra-Host Evolution (LASSIE) Identifies Immune-Selected HIV Variants},
  journal = {Viruses},
  year = {2015},
  volume = {7},
  number = {10},
  pages = {5443-5475},
  author = {Peter Hraber and Bette Korber and Kshitij Wagh and Elena E. Giorgi and Tanmoy Bhattacharya and S. Gnanakaran and Alan S. Lapedes and Gerald H. Learn and Edward F. Kreider and Yingying Li and George M. Shaw and Beatrice H. Hahn and David C. Montefiori and S. Munir Alam and Mattia Bonsignori and M. Anthony Moody and Hua-Xin Liao and Feng Gao and Barton F. Haynes},
  url = {http://mdpi.com/1999-4915/7/10/2881},
}
```

***