InterProScan domain annotation of PKZILLA polypeptides

This is a .zip archive of the git repository and Nextflow workflow used for annotation of the PKZILLA protein domains using InterProScan. In brief, all possible InterProScan searches were performed via the latest InterProScan Docker container, with post-processing to remove certain redundant and overlapping PKS domain annotations. For further details, see archived files and code, and manuscript Materials and Methods.

The Nextflow ./work directory is not included to reduce complexity. Nextflow published results are available in ./results . 

See also: https://doi.org/10.5281/zenodo.10011739 , for analogous predictions but for all the non-PKZILLA annotated proteins from Prymnesium parvum 12B1. 

Key files:

• ./run.sh entry script for running InterProScan on PKZILLA-1,-2,-3
• GFF3 file of InterProScan features, after post processing: './results/gff_nested_filter/filtered/ipr_merged.gff'
• PDF of all features on PKZILLA-1, unnormalized length: './results/pdf_2_PDF_A_1B/output/PKZILLA-1.gff.dfv.svg.pdf'
• PDF of all features on PKZILLA-2, unnormalized length: './results/pdf_2_PDF_A_1B/output/PKZILLA-2.gff.dfv.svg.pdf'
• PDF of all features on PKZILLA-3, unnormalized length: './results/pdf_2_PDF_A_1B/output/PKZILLA-2.gff.dfv.svg.pdf'
• ./run2.sh entry script for performing a "beads on a string" figure generation, where representative domains are selected and length normalized.
• PDF of selected diagnostic PKS domain features on PKZILLA-1 with normalized length: './results/beads_on_string:svg_2_pdf/1_PKZILLA-1.gff.dfv.svg_2_PKZILLA-1.gff.dfv.svg_3_PKZILLA-1.gff.dfv.svg_4_PKZILLA-1.gff.dfv.svg_5_PKZILLA-1.gff.dfv.svg_compose.svg.pdf'
• PDF of selected diagnostic PKS domain features on PKZILLA-2 with normalized length: '/results/beads_on_string:svg_2_pdf/1_PKZILLA-2.gff.dfv.svg_2_PKZILLA-2.gff.dfv.svg_3_PKZILLA-2.gff.dfv.svg_4_PKZILLA-2.gff.dfv.svg_compose.svg.pdf'
• PDF of selected diagnostic PKS domain features on PKZILLA-3 with normalized length: '/results/beads_on_string:svg_2_pdf/1_PKZILLA-3.gff.dfv.svg_2_PKZILLA-3.gff.dfv.svg_3_PKZILLA-3.gff.dfv.svg_compose.svg.pdf'