Explore projects

NCBI taxonomy dump parser

Simulation pipeline for generation of artificial polyploid genomes, estimation of their haplotypes from Next Generation Sequencing data using HapTree, HapCompass and SDhap, and finally evaluation of the estimation accuracy.

Visualize genes in a GenBank file as arrows in SVG format.

ibrowser

Simulation pipeline for generation of artificial polyploid genomes, estimation of their haplotypes from Next Generation Sequencing data using HapTree, HapCompass and SDhap, and finally evaluation of the estimation accuracy.

Biosynthetic Genes Similarity Clustering and Prospecting Engine.

Defines a distance metric between Gene Clusters using a combination of three indices (Jaccard index, a modified Domain Duplicate Score and the Goodman-Kruskal gamma function)

CIHEAM course material

A script for retrieval of SMILES chemical data of compounds produced by Biosynthetic Gene Clusters. Data is gathered from the MIBiG repository (single package with all entries in JSON format)

Arabidopsis eQTL analysis platform

Scripts and resources used for my MSc Thesis at the Bioinformatics chair group.

The goal this project is to create a pipeline that automates the secondary metabolite phylogenetic analysis of fungi to a certain extent.

A concept for a BrAPI discovery node. Written in Python, Flask-based.