AbNumber

Convenience Python APIs for antibody numbering and alignment usingANARCI

Try it out in your browser using Binder:

Features:

• Streamlined Python APIusingChainobject
• Identifying CDR regions,e.g. usingchain.regionsorchain.cdr3_seq
• Inde xing and slicing,e.g. usingchain['5']orchain['H2':'H5']
• Pairwise and multiple sequence alignmentin the given numbering usingchain.align(another)
• Alignment to nearest human germlineusingchain.align(chain.find_merged_human_germline())
• Humanization using CDR graftingbychain.graft_cdrs_onto_human_germline()

SeeAbNumber Documentationfor the full reference.

Installation

Install using Bioconda:

conda install -c bioconda abnumber

Note:Windows is not supporteddue toHMMERdependency. AbNumber is currently only available on UNIX & MacOS.

Examples

fromabnumberimportChain

seq='QVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYDDHYCLDYWGQGTTLTVSSAKTTAPSVYPLA'
chain=Chain(seq,scheme='imgt')

chain
# QVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYDDHYCLDYWGQGTTLTVSS
# ^^^^^^^^ ^^^^^^^^ ^^^^^^^^^^^^

chain.cdr3_seq
# ARYYDDHYCLDY

chain.print(numbering=True)
# 0 1 2 3 4 5 6 7 8 9 10 11 12
# 12345678912345678901234567890567890123456789012345678923456789012456789012345678901234567890123456789023456789012345678
# QVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYDDHYCLDYWGQGTTLTVSS
# ^^^^^^^^ ^^^^^^^^ ^^^^^^^^^^^^

Chain can be iterated:

forpos,aainchain:
print(pos,aa)
# H1 Q
# H2 V
# H3 Q
# H4 L
# H5 Q

Chain can also be indexed and sliced using scheme numbering:

chain['5']
# 'Q'
forpos,aainchain['H2':'H5']:
print(pos,aa)
# H2 V
# H3 Q
# H4 L
# H5 Q

For all methods seeAbNumber Documentation

Credits

SeeANARCI on GitHuband the ANARCI paper:ANARCI: antigen receptor numbering and receptor classification