When: 22nd May 2025 | 14.00 -15:30 GMT
The International Barley Hub is pleased to announce the next seminar in its 2025 series, run by leading barley scientists and industry experts. This seminar will be presented by Patrick König (Research Associate, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Germany).
Summary:
PanBARLEX is a web portal that offers convenient access to 3,797,824 predicted genes, their functional annotations and homology clusters of 76 different barley genotypes that together define a pan-genome for barley. The portal offers versatile entry points, including the ability to quickly open gene cards by gene-IDs, conduct full text index searches based on functional annotations and perform homology search of proteins through a BLAST database search using user-defined DNA or amino acid query sequences. Additionally, a multi-way gene-ID lift-over tool is available, enabling the conversion of gene-IDs between multiple assembly versions of the reference genotype “Morex”. To enhance user exploration of the structural variation of genes, the portal provides a qualitative beeswarm plot like visualization of the physical positions of all homologous genes of a homology cluster. An interactive viewer for precalculated multiple sequence alignments and phylogenetic trees of homology clusters allows to quickly inspect the DNA and amino acid sequence diversity for homologous genes. The expression data of the barley pan-transcriptome project is integrated with the homology clusters and can be visualized via heatmaps of TPM values. To support ad-hoc analysis of sequence diversity, the portal offers interactive pairwise Smith-Waterman alignments of sequences. Interactive self-aligned and pairwise-aligned dot plots are available for DNA sequences of assembled chromosomes, providing ad-hoc insights into sequence similarity and diversity. Furthermore, users can download sequences of all genes within a homology cluster as multi-FASTA files, supporting downstream applications like customized multiple sequence alignments. PanBARLEX serves as a comprehensive and valuable resource, combining extensive gene annotations, user-friendly entry points and useful analytical tools to advance research and understanding of the pan-genomic diversity of barley. The tool is publicly available at this URL: https://panbarlex.ipk-gatersleben.de
Speakers bio:
Patrick König:
- he studied hydrology at Dresden University of Technology where he graduated 20214 with a diploma degree in hydrology
- worked full-time as freelancer for full stack web development until 2017
- since 2017 working as a research assistant specialized in research software engineering in the Bioinformatics and Information Technology group headed by Dr. Uwe Scholz at IPK Gatersleben
- worked on the IPK project “BRIDGE”, which focused on the utilization of the entire barley collection of the IPK gene bank, resulting in the development of the “BRIDGE web portal” (https://bridge.ipk-gatersleben.de)
- developed the web-based tool “DivBrowse” for interactive visualization and exploratory data analysis of variant call matrices (https://divbrowse.ipk-gatersleben.de)
- currently working in the IPK project “SHAPE-P3” which focuses on the structural variation and haplotype diversity of the barley pan-genome
- currently co-lead of the measure “M4.4 – Scientific Workflow Infrastructure (SciWIn)” of the german NFDI (National Research Data Infrastructure) consortia “FAIRagro” (https://fairagro.net)