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  "Title": "Identification of domain isotypes in pfam data",
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  "Description": "Protein domains is one of the most import annoation of\nproteins we have with the Pfam database/tool being (by far) the\nmost used tool. This R package enables the user to read the\npfam prediction from both webserver and stand-alone runs into\nR. We have recently shown most human protein domains exist as\nmultiple distinct variants termed domain isotypes. Different\ndomain isotypes are used in a cell, tissue, and\ndisease-specific manner. Accordingly, we find that domain\nisotypes, compared to each other, modulate, or abolish the\nfunctionality of a protein domain. This R package enables the\nidentification and classification of such domain isotypes from\nPfam data.",
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  "Date/Publication": "2026-04-28 13:00:52 UTC",
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    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
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