Table 1 Description of PDAUG tools. PDAUG toolset comprises 24 different tools across 9 functional categories
Functionality | Tool name | Major libraries used |
|---|---|---|
Data visualization and plotting | PDAUG basic plots | matplotlib*, pandas*, seaborn*, quantiprot |
PDAUG fishers plot | ||
PDAUG peptide data plotting | ||
PDAUG peptide Ngrams | ||
PDAUG sequence network | ||
PDAUG peptide length distribution | ||
PDAUG uversky plot | ||
Descriptor calculation | PDAUG AA property based peptide descriptor | modlAMP, pandas, pydpi |
PDAUG peptide core descriptors | ||
PDAUG peptide global descriptors | ||
PDAUG sequence property based descriptors | ||
PDAUG word vector descriptor | ||
Peptide library generation | PDAUG AA property based peptide generation | modlAMP, pandas |
PDAUG sequence based peptide generation | ||
ML | PDAUG ML models | sklearn*, matplotlib, seaborn, pandas, gensim, nltk |
PDAUG word vector model | ||
Circular dichroism (CD) data analysis | PDAUG peptide CD spectral analysis | modlAMP, pandas |
Peptide 3D structure | PDAUG peptide structure builder | fragbuilder, pandas |
Core functionality | PDAUG peptide sequence analysis | modlAMP, pandas |
PDAUG peptide core functions | ||
Peptide data access | PDAUG peptide data access | modlAMP, biopython, pandas |
Data handling and IO | PDAUG TSVtoFASTA | pandas |
PDAUG merge dataframes | ||
PDAUG AddClassLabel |