Kazanov Lab

Software & Tools

The lab develops freely available bioinformatics software for the research community. Source code is hosted on GitHub.

GKclust — detection of mutation clusters in genomes

A computational tool for detecting clusters of somatic mutations in complete genomes. Analyzes VCF files to identify mutational hotspots with configurable statistical thresholds; supports SNVs, indels, or both.

GitHub
GKsims — simulation of somatic mutations for different mutagens

Generates realistic somatic mutations for mutagens such as APOBEC and UV radiation, sampling across genomic features including replication timing, gene/intergenic regions, and transcription/replication strand.

GitHub
RNAsselem — analysis of RNA secondary structure elements in viral genomes

A Python package for analyzing RNA secondary structure elements in viral genomes. Converts between structure formats (dot-bracket, CT, WUSS), classifies nucleotides into structural categories (stems, loops, bulges, etc.), and produces statistical summaries of element frequency and size distributions.

GitHub Reference paper
ProteaseSpecificityModels — prediction of protease cleavage sites by PWM

Calculates proteolytic susceptibility scores using position-weighted matrices (PWMs) for 169 proteases from the MEROPS database. Takes protein sequences in FASTA format and outputs per-position PWM scores.

GitHub Reference paper
ProteolysisStructuralPrediction — structural susceptibility of proteins to proteolytic cleavage

Estimates the susceptibility of protein regions to proteolytic cleavage based on 3D structure. Supports both experimental PDB structures and AlphaFold models. Assigns a 0–1 susceptibility score to each peptide bond and generates color-mapped 3D visualizations.

GitHub Reference paper