Explore projects

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)

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

ibrowser

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.

Calculate the diversity of your gene clusters! Using hmmscan to find the pfam domains. Jaccard, DDS, GK as distance metrics including sequence similarity as a modifier. It outputs tab delimited network files that can be visualized in Cytoscape.

Arabidopsis eQTL analysis platform

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

Biosynthetic Genes Similarity Clustering and Prospecting Engine.

Defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency Index)

Biosynthetic Genes Similarity Clustering and Prospecting Engine.

Defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency Index)

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.

Find SNPs in putative TFBS that change the expression of the nearby gene

A convolutional neural network for the purpose of interpretable protein-protein interaction prediction.