GitHub - jamesc0/primer-dimers

Branches Tags

Name		Name	Last commit message	Last commit date
Latest commit History 44 Commits
data		data
visualisation		visualisation
.gitignore		.gitignore
3_prime_end_testing.cc		3_prime_end_testing.cc
3_prime_end_testing_out.txt		3_prime_end_testing_out.txt
LICENSE.md		LICENSE.md
Makefile		Makefile
README.txt		README.txt
j-mer_testing_results.txt		j-mer_testing_results.txt
jmer_counting.cc		jmer_counting.cc
lcs_dp.cc		lcs_dp.cc
lcs_dp_out.txt		lcs_dp_out.txt
main.cc		main.cc
main_coarse.cc		main_coarse.cc
sequence_functions.cc		sequence_functions.cc
sequence_functions.h		sequence_functions.h

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An algorithm which, given a list of primers, returns primer dimer candidates.

Compile using

make main

Run using

./main data/data.txt > out.txt

replacing data/data.txt with the name of the input file.
The input file should be formatted like the file at data/data.txt
The parameters can be changed in lines 12-17 of the main.cc code

The algorithm takes 5.6 seconds to run on 200 candidate primers.
The running time should grow quadratically with the number of candidate primers.