Output from Import Immune Reference Segments

The importer outputs a sequence list that can be used for immune repertoire analysis. These can be added to a custom reference data set, to be used in workflows. See http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Custom_Sets.html for details.

The sequence list contains the reference sequences for the V, D, J and C segments, named in the format <chain>-<type>-<ID>*<allele>, for example "TRA-V-1*01". Note that for B cells constant genes, the letter corresponding to the encoded isotype will be used instead of the segment type.

If the gene segment does not have an allele or Import only the first allele is ticked, *<allele> is not added to the name.

By ticking "Show annotations" and "Region" in the Side Panel "Annotation layout" and "Annotation types" groups, respectively, the location of the conserved amino acid can be visualized (see figure 7.4).

Image ref_seq_motif_view
Figure 7.4: Visualizing the location of the conserved amino acid.

The table view of the sequence list shows the chain and segment type of each sequence, and for the IMGT format, also the accession number(s) and species (see figure 7.5).

Image ref_seq_table_view
Figure 7.5: Table view of imported sequence list showing the name, species and accession number when imported using the IMGT format.