NBDC/DBCLS BioHackathon 2022, Kochi, Japan

  BH22JP 

Preprints

• Mar 15, 2023

  Comparison of orthology finding tools using plant genes

  Orthology finding tools are valuable for analyzing biological data from multiple species and predicting the functions of uncharacterized genes. Although several tools are available for this purpose, the characteristics of their results for plant genes are not well compared. In this hackathon, we examined three tools (OMA, OrthoDB, and Ensembl Plants) by extracting ortholog pairs between Arabidopsis and soybean and analyzing each result, focusing on five plant genes with varying degrees of conservation. We observed that changes in the taxonomic ranges of OMA and OrthoDB affected ortholog detection, and the range of ortholog detection across the three tools was inconsistent, suggesting the importance of comparing multiple tools to obtain more accurate information on orthologs. less than 1 minute read
• Sep 27, 2022

  GEM: Genome Editing Meta-database

  Genome editing is a widely used tool to create precise changes in a genome. However, no specialized database for genome editing is available. Therefore, we have been developing genome editing meta-database (GEM) which aims to collect the exhaustive dataset of metadata related to genome editing. Currently, GEM consists primarily of a subset of genome editing- related metadata from PubMed articles. Metadata is extracted from research articles that have the contents with experiments using either of 7 types of genome editing tools: CRISPR-Cas9, Transcription activator-like effector nuclease (TALEN), Zinc finger nuclease (ZFN), CRISPR- Cas12, CRISPR-Cas3, Base editor, and Prime editor. Those tools are often used for knock-out or knock-in of genes to elucidate the biological functions of them. In domestic version of BioHackathon in 2022 (BH22.9), we have discussed the datasets and the usage of GEM, and also updated the scripts for GEM in github based on the discussion. less than 1 minute read