SelectiveGenomeAmplification
============================

PI: http://brisson.bio.upenn.edu/

To use this you'll need:

 - A unix environment
 - kmer_total_count, a kmer counter available here: http://github.com/mutantturkey/dna-utils/
 - bash or compliant shell.
 
 
Setup:

    git clone git@github.com:mutantturkey/SelectiveGenomeAmplification.git
    cd SelectiveGenomeAmplification
    make
    sudo make install

Example Usage:

    selectiveGenomeAmplification PfalciparumGenome.fasta HumanGenome.fasta;
    less PfalciparumGenome_HumanGenome/final_mers

For user customizable variables:

    max_mer_distance=5000 max_select=6 min_mer_range=6 max_mer_range=12 \
    SelectiveGenomeAmplification.sh PfalciparumGenome.fasta half.fasta 

## Customizable variables

range of mers, min and max 

variable | default | notes
:---- | :---- | ---- | :----
min\_mer\_range | 6  | minimum mer size to use
max\_mer\_range | 12 | maximum mer size to use 
max\_mer\_distance | 5000 | maximum distance between mers in foreground
output\_directory | $PWD/$foreground\_$background/ | ex. if fg is Bacillus.fasta and  bg is HumanGenome.fasta then folder would be $PWD/Bacillus.fasta\_HumanGenome\_output.fasta/
counts\_directory | $output\_directory/.tmp | directory for counts directory
tmp\_directory=$output\_directory/.tmp | temporary files directory
max\_melting\_temp | 30° | maximum melting temp of mers
min\_melting\_temp | 0° | minimum melting temp of mers
min\_foreground\_binding\_average | 50000 | elminate mers that appear less frequently than the average  (length of foreground / # of occurances)
max\_select | 15 | maximum number of mers to pick
max\_check | 35  | maximum number of mers to select (check the top #)
ignore\_mers | Not Enabled | mers to explicitly ignore, space seperated ex. ignore\_mers="ACAGTA ACCATAA ATATATAT"
foreground | Not Enabled | path of foreground file
background | Not Enabled | path of background file
max\_consecutive\_binding | 4 | The maxium number of consecutive binding nucleotides in homodimer and heterodimers
fg\_weight | 0 | How much extra weight to give higher frequency mers in fg. see "equations"

## Equations

Here's what we are using to determine our scoring and selectivity

### Selecivity

Our selectivity is what we use to determine what top $max\_check mers are checked later
on in our scoring function. Currently we use this formula:

By default our fg\_weight is zero. This gives no extra weight to more
frequently occuring mers, but can be set higher with the fg\_weight
environmental variable if you wish to do so.

    hit = abundance of primer X (ex. 'ATGTA') in background

    (foreground hit / background hit) * (foreground hit ^ fg_weight)