Bioinfo_toolbox

Prepare steps

This toolbox requires Biopython and msms packages (msms is required only for computing structure related properties, it is used by Bio.PDB.ResidueDepth module). You can install them with conda. Alternatively, install Biopython using pip and install msms manually.

Create conda environment and install needed packages

create an environment conda create --name toolbox

activate it conda activate toolbox

add bioconda channel conda config --add channels bioconda

install necessary packages conda install biopython msms

Pip and manual installation

Biopython

create python virtual environment python -m venv toolbox

activate it source bioinf/bin/activate

install Biopython pip install msms biopython

msms

Download msms tool from: http://mgltools.scripps.edu/downloads#msms based on your OS. After the installation, make sure that msms is in your PATH variable.

Clone this repository

git clone "https://github.com/CalounovaT/Bioinfo_toolbox/"

Run the toolbox

run the main program ./main.py

1) Processing FASTA files

Obtain description of an entry given its index in a file (0 in the example below)

./main.py fasta --description 0 proteins.fasta

Obtain sequence of an entry given its index in a file (0 in the example below)

./main.py fasta --sequence 0 proteins.fasta

Return sequence length given its index in a file (0 in the example below)

./main.py fasta --length 0 proteins.fasta

Return subsequence of a sequence given its index in a file, subsequence start and end positions

./main.py fasta --subsequence 0 1 6 proteins.fasta

2) Measuring sequence similarity using Hamming distance

Measure Hamming distance of two sequences

./main.py hamming 'ABC' 'ACC'

3) Sequence alignment using edit distance

Measure the edit distance of two sequences

./main.py edit 'ABC' 'AAC'

Output their alignments

./main.py edit --alignment 'ABC' 'AAC'

4) Processing PDB files

Obtain information about the stored structure (number of models, structures, residues, atoms).

./main.py pdb --information 1B0B.pdb

Comptue the width of the structure (maximum of distance of any two atoms).

./main.py pdb --width 1B0B.pdb

Obtain list of atoms being in given distance from given ligand (HETATM). - give ligand and distance as arguments

./main.py pdb --atoms SAC 10 1B0B.pdb

Obtain list of residues being in given distance from given ligand (HETATM).

./main.py pdb --residues SAC 10 1B0B.pdb

5) Processing multiple sequence alignment

Retrieve sequence by its position

./main.py msa --sequencepos 0 align.msa

Retrieve sequence by its id

./main.py msa --sequenceid "UniRef90_UPI000" align.msa

Retrieve given column from the MSA

./main.py msa --column 0 align.msa

Retrieve sum of pairs score of a column

./main.py msa --spcolumn 0 align.msa

Retrieve sum of pairs score of a msa

./main.py msa --spmsa align.msa

6) Conservation determination from multiple aligned sequences

Compute conservation of all positions in the msa

./main.py conservation --conservation align.msa

identify top N scoring positions in the msa

./main.py conservation --toppositions 5 align.msa

7) Computing structure-related properties

Compute the diameter of the protein.

./main.py properties --diameter 1B0B.pdb

Compute the ratio of surface and buried amino acids.

./main.py properties --ratio 1B0B.pdb

Output data for a histogram of amino acids composition of buried and exposed amino acids.

./main.py properties --surfacecounts 1B0B.pdb

./main.py properties --buriedcounts 1B0B.pdb

Quantify portion of polar amino acids in the core and on the surface of the protein.

./main.py properties --surfacepolar 1B0B.pdb

./main.py properties --buriedpolar 1B0B.pdb