Algorithms in Bioinformatics - Sequences Q1/2015

By Martin Storgaard, Konstantinos Mampentzidis and Henrik McQuoid Jespersen

This project is about implementing and experimenting with pairwise sequence comparison methods to compute optimal global alignments of two sequences where the object is to minimize a cost.

How to compile

This project depends on cmake version 3.2 and is only tested on Ubuntu 14.04. To get the latest cmake run the following:

sudo add-apt-repository ppa:george-edison55/cmake-3.x
sudo apt-get update

If cmake is already installed, use: sudo apt-get upgrade, otherwise use sudo apt-get install cmake

To compile all sources, run ./make.sh (or the usual cmake command, the bash scripts ensures uniformity).

The main found is now located in build/bin.

How to run a single algorithm

./executable [all,global_linear,global_affine] seq1 seq2

Available algorithms: global_linear, global_affine