We have fixed a problem with the amino acid alignment of some V sequences in the macaque IGL set. This impacts the gapping of the V sequences (but not the nt sequence itself) and consequently changes the delineation of CDR1 and CDR2 in those sequences (the delineation of the start of CDR3 was not affected).… Continue reading Macaque sets updated
Category: OGRDB_News
Rhesus Macaque IG Germline sets released
The Germline Database Working Group of the AIRR Community is pleased to announce publication on OGRDB of rhesus macaque germline sets covering all three IG loci. These sets include IG sequences from the recent publication in Immunity, “Population-level genomic analysis of immunoglobulin loci variation in rhesus macaques reveals extensive germline diversity” [1], derived from 106… Continue reading Rhesus Macaque IG Germline sets released
Human IGHC set released
We’re pleased to publish the first version of a human IGHC germline set on OGRDB. The set is based on the work of Jana et al., 2025, and contains 105 full-length IGH constant region sequences, derived from long-read genomic sequencing. This work substantially increased the number of published sequences and revealed significant polymorphism and population… Continue reading Human IGHC set released
New publication
Please read our update article in Nucleic Acids Research to learn about new features in OGRDB and VDJbase, and plans for the future. William D Lees, Ayelet Peres, Vered Klein, Naama Amos, Uddalok Jana, Eric Engelbrecht, Zachary Vanwinkle, Yaniv Malach, Thomas Konstantinovsky, Pazit Polak, Corey T Watson, Gur Yaari, The current landscape of adaptive immune… Continue reading New publication
Uploading germline sets to OGRDB
Germline sets, or additional data for existing sets, is provided in two CSV files which are uploaded to the site. This repo documents file formats and the process to follow in creating them. It also provides a number of utilities which are designed to simplify data creation and to check the data before upload.
Contributing germline sets to OGRB
We welcome submissions of germline sets for new species, and new sequences for existing species. Under our overall policy, expressed in the name of the site, contributions must be free for anyone to use. OGRDB is structured to allow individuals or groups to manage the sets that they provide, and we hope that they will… Continue reading Contributing germline sets to OGRB
Gene Tables and Alignments!
This month we’ve added gene tables and alignments to OGRDB. Both can be reached from the Sequences dropdown at the top of every page. Gene Tables list all the sequences in a locus, organised by gene. You can click on the sequence name to see full details of the sequence, including the support we have… Continue reading Gene Tables and Alignments!
Website updated
We have redesigned the front page and added a new help page which brings together all information on how to use OGRDB. Other pages have been restyled to make them simpler and easier to use. We hope you will enjoy the new site. If there are any problems, please let us know by using the… Continue reading Website updated
OGRDB API v2
The OGRDB API has been upgraded to provide new features: This guide describes the new API. The old API is still available for compatibility with existing scripts.
Additional support for germline sets
We have created step-by-step walk-throughs showing how to use the AIRR-C germline sets with local installations of IgBLAST and MiXCR. These tools make use of download_germline_set, which is a powerful command-line utility which can be used to download sets in various formats, and explore the sets and versions available in OGRDB. It can even create… Continue reading Additional support for germline sets