Pairwise sequence alignment using Hidden Markov Models
Project repository for Bioinformatics course at Faculty of Electrical Engineering and Computing, University of Zagreb, 2018./2019.
Main goal of this project is implementation of an algorithm for pairwise sequence alignment using HMM.
Clone this repo and go to ./build directory
git clone [email protected]:Sokre95/bioinf_project.git
cd bioinf_project/build
Build bioinf executable
make
Execute ./bioinf --help to print command info
Run either with -v [--viterbi] or -e [--estimate] option. Both options can't be used at the same time
Usage:
bioinf [OPTION...]
OPTIONS options:
-v, --viterbi arg # Run sequence alignment algorithm on sequence pair given in fasta file
specified by <arg> path
-e, --estimate arg # Run HMM parameters estimator with path to directory holding learning database
specified by <arg> path. Calculated parameters are stored in ./params.txt file
-o, --out arg # [Use only with -v option] Write aligned sequences to ./aligned/{pair_file_name}.fasta
(default: true)
-c, --console # [Use only with -v option] Print aligned sequences to console
-m, --multiline [=N(=100)] # [Use only with -v option] Write/Print aligned sequences in multiple lines, each line
containg N chars
-p, --progress # Show progress while running algorithm
-t, --mem-optimized # Run memory optimized version of Viterbi algorithm
-h, --help # Show help
All input files must be in FASTA format and can be placed in arbitrary location. You always have to specify path to the file or folder you are using.
Run sequence alignment for p2.fasta file writing 200 chars in each line of output file and print output to console also
./bioinf --viterbi ../database/pairs/hepatitis/p2.fasta --console --multiline=200 --progress
Estimate HMM parameters (probabilities) using outputs_mafft/upcase as learning database
./bioinf --estimate ../database/outputs_mafft/upcase
All c++ files are located in /src and /include folder. In /helpers folder are small python and ruby scripts used as a help in development of this project.
2018 Tomislav Božurić, Krešimir Topolovec & Martin Pisačić
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