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Examples

IgMAT can be used to annotate sequences with the default IMGT dataset, or specific datasets can be created:

Annotating a sequence

To annotate an input sequence with the default IMGT database:

igmat run -i DVQLVESGGGSVQAGGSLRLSCAVSGSTYSPCTTGWYRQAPGKEREWVSSISSPGTIYYQDSVKGRFTISRDNAKNTVYLQMNSLQREDTGMYYCQIQCGVRSIREYWGQGTQVTVSSHHHHHH -v

It will print a representation of the annotated sequence:

Query 'Input sequence':

 HMMR match: Vicugna+pacos_H [eValue: 2.000e-55]

   0 -----------FR1------------|----CDR1----|-------FR2-------|---CDR2---|-  70
   0 DVQLVESGG-GSVQAGGSLRLSCAVS|GSTY----SPCT|TGWYRQAPGKEREWVSS|ISSP---GTI|Y  70

  70 -----------------FR3------------------|-----CDR3----|----FR4----| 135
  70 YQDSVK-GRFTISRDNAKNTVYLQMNSLQREDTGMYYC|QI-QCGVRSIREY|WGQGTQVTVSS| 135

Creating a custom dataset

To create a custom dataset, input files with sequences from V and J regions are needed, where the name of the files must adhere the following format:

	<name>_<chain><type>

Where name is a species or sample name, and type is either V or J. An example of input sequences for generating custom datasets is distributed in the test/build folder:

igmat build -i ./test/build -n cattle

The command will generate a cattle dataset that will be available to be used with IgMAT with the command:

igmat run -i DVQLVESGGGSVQAGGSLRLSCAVSGSTYSPCTTGWYRQAPGKEREWVSSISSPGTIYYQDSVKGRFTISRDNAKNTVYLQMNSLQREDTGMYYCQIQCGVRSIREYWGQGTQVTVSSHHHHHH -m cattle