Clone Annotation Block
Trace reading, merging and alignment use Tracy, part of GEAR Genomics and developed at EMBL. If you use this block in your research, please cite:
Rausch, T., Fritz, M. H., Untergasser, A., & Benes, V. (2020). Tracy: basecalling, alignment, assembly and deconvolution of sanger chromatogram trace files. BMC Genomics 21, 230. https://doi.org/10.1186/s12864-020-6635-8
MiXCR is developed by MiLaboratories Inc. It aligns each sequence to germline genes. For more information, please see the MiXCR website and cite:
Bolotin, D., Poslavsky, S., Mitrophanov, I. et al. MiXCR: software for comprehensive adaptive immunity profiling. Nat Methods 12, 380–381 (2015) https://doi.org/10.1038/nmeth.3364
Residue numbering, region boundaries and the chain call use ANARCI:
Dunbar J and Deane CM. ANARCI: antigen receptor numbering and receptor classification. Bioinformatics, 32(2):298-300 (2016). https://doi.org/10.1093/bioinformatics/btv552