Lab Software

Tools Empowering Genomic Discovery

We design and maintain open-source software for handling large-scale genomic data, revealing DNA structural patterns, and streamlining computational biology workflows. Explore the toolset that supports our collaborators and the wider scientific community.

Featured resources

From scalable k-mer analytics to structural motif detection, each tool includes documentation and ready-to-use code to integrate with your pipelines.

MAFin: Motif detection in multiple alignment files

MAFin is a tool for finding conserved motifs directly within multiple alignment files (MAF format). It supports three modes of motif specification: (i) exact k-mers provided by the user, (ii) patterns defined via regular expressions, and (iii) position-weight matrices (PWMs). After motif detection, MAFin computes conservation statistics across aligned sequences, quantifies conservation percentages, and outputs results in JSON or CSV for downstream analysis.

Keywords

motif detection
MAF format
conservation analysis
genomic motifs

Highlights

First tool to detect motifs inside MAF alignment files directly
Supports motif specification via k-mers, regex, or PWMs
Calculates conservation across aligned sequences and outputs conservation percentage metrics
Exports results in JSON / CSV formats for downstream use

Key features

Input: MAF alignment files
Motif specification: exact k-mers, regex, or PWMs
Outputs motif occurrences and conservation levels
Exports results in JSON and CSV
Supports large alignment files with efficient parsing

ZSeeker: An optimized algorithm for Z-DNA detection in genomic sequences

ZSeeker is a novel computational algorithm designed to identify potential Z-DNA forming sequences within genomic DNA. Z-DNA is an alternative left-handed DNA helix with a zigzag backbone, distinct from canonical B-DNA, and has been implicated in processes such as transcription, replication, DNA repair, and genetic instability. ZSeeker improves upon prior approaches in terms of computational efficiency, usability, and interpretability, and is provided both as a Python package and via a web interface to facilitate accessibility.

Keywords

Z-DNA
non-B DNA structure
genomic sequence analysis
computational detection

Highlights

Detects potential Z-DNA-forming sequences in genomic data
Addresses limitations of earlier methods (efficiency, usability, interpretability)
Offered as both a standalone Python package and web interface
Allows users to adjust detection parameters and provides output visualization

Key features

Input: Genomic sequences (FASTA and similar)
Detection algorithm optimized for Z-DNA motifs
Configurable detection thresholds and scoring system
Output includes Z-DNA loci with Z-scores
Available as Python package and web-based interface

MAFcounter: An efficient tool for counting the occurrences of k-mers in MAF files

MAFcounter is the first k-mer counting tool specifically designed to operate on alignment files in the MAF (Multiple Alignment Format). It supports DNA and protein alignments, is multithreaded, fast and memory-efficient, and offers a versatile set of features for k-mer analysis directly in alignment context. It fills a gap because existing k-mer counters typically work on raw sequence data (e.g. FASTA) rather than alignments.

Keywords

k-mer counting
multiple alignment
MAF format
genomics
proteomics

Highlights

Dedicated k-mer counting in MAF alignment files (DNA and protein)
Multithreaded and memory-efficient implementation
Provides a wide variety of k-mer analysis features
Open-source under GPL, available on GitHub

Key features

Input: MAF alignment files
Counts DNA and protein k-mers
Supports customizable k lengths
Parallelized (multithreading) for performance
Light memory footprint compared to standard k-mer counters