For example: IGHV1-1*01 or IGL_myGeneName would both work. Alternatively, each reference sequence should contain an annotation named V-region or J-region or D-region ( V_segment, J_segment and D_segment type, respectively) as well as a gene property starting with the prefix IGH (for heavy chain) or IGL or IGK (for light chain).Annotating the entirety of each heavy chain sequence with VDJ-region and light chains with VJ-region annotation names (using a CDS annotation type).This can be accomplished in one of the following ways: In particular, Antibody Annotator needs to know whether sequences are from heavy or light chains and where Framework/CDR regions are within each sequence to enable the annotation of novel sequences.Īntibody Annotator requires all sequences to be identifiable as heavy or light chain. In order to create a custom reference sequence database, the reference sequences will have to satisfy some requirements to be able to be read by Antibody Annotator. Some amount of sequence ambiguities is tolerated, particularly in the centre of CDR/FR regions. They could also represent non-germline parent sequences or scaffolds, so long as these sequences are Ig-like in nature and structure. These custom sequences could represent germline genes of the Ig/TCR variable region of one or more species.
The most appropriate FR/CDR region boundaries, calculated from the whole dataset not just the closest match.The closest matching reference gene(s) to each of your target sequences, and what the silent and non-silent variations in the target sequence are relative to its closest match.
#GENEIOUS VS GENEIOUS PRIME HOW TO#
Please refer to the following article for more information about the different types of reference database, and how to upload correctly formatted sequences into a reference database.Ĭreating reference databases for Antibody AnnotatorĪntibody Annotator uses (germline) reference sequences to determine two key aspects of sequence annotation: It describes how to annotate and package the sequences in the correct format. This article deals specifically with creating germline-style reference sequences for Antibody Annotator. The analysis operations that allow or expect a reference database will contain a dropdown listing the reference databases available to you.
As a user of Biologics, you can select custom reference sequence databases for use in analyses.
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