When: Thu, 30 May 2024 14:00 – 15:30 BST
The International Barley Hub is pleased to announce the next in the 2024 series of seminars: ‘PanBarlex – A Comprehensive Resource of Gene Annotations and Orthogroups of the Barley Pan-genome’ presented by Patrick König (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Germany).
Speakers bio:
Patrick König
Patrick studied hydrology at Dresden University of Technology he graduated in 2014 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 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)
Summary:
PanBARLEX is a web portal that offers convenient access to gene annotations and orthologous gene groups of 76 different barley genotypes that together define a pan-genome. The portal encompasses a total of 3,797,824 annotated genes, with 3,730,725 genes identified as orthologs grouped into 95,237 orthogroups determined through an analysis with OrthoFinder. The portal features versatile entry points, including the ability to locate genes by their IDs, conduct searches based on functional annotations and perform gene queries through a BLAST database search using user-defined DNA or amino acid query sequences. Additionally, a precalculated BLAST-based lift over is available, enabling conversion of established Morex V3 gene IDs to Morex pan-genome gene IDs. 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 orthologs within an orthogroup. To facilitate further analysis, the portal offers online pairwise Smith-Waterman alignments between sequences, providing valuable insights into sequence similarities. Furthermore, users can download sequences of all genes within an orthogroup as multi-FASTA files, supporting downstream applications like multiple sequence alignment. 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 barley pan genome. The tool is publicly available at this URL: https://panbarlex.ipk-gatersleben.de