Integrated computational AMP discovery pipeline reveals novel helminth AMP-like peptides.

A) Summary of homology directed approach using lophotrochozoan-derived AMPs. i) Breakdown of lophotrochozoan AMP database by phylum. ii) Breakdown of lophotrochozoan AMP database by AMP family. Asterisk indicates that multiple algorithms were used for each AMP prediction tool. B) Summary of computational helminth AMP prediction approach. i) The number of nematode AMP-LPs and percentage of prediction tools indicating antimicrobial potential. ii) The number of flatworm AMP-LPs and percentage of prediction tools indicating antimicrobial potential. iii) The number of peptides in each group after AMP-LPs were organised into groups. AA, Amino acid; ADAM, A Database of Antimicrobial Peptides; AMP, Antimicrobial Peptide; AMP-LP, Antimicrobial Peptide-like Peptide; APD, Antimicrobial Peptide Database; APS, Antimicrobial Peptide Scanner; BLAST, Basic Local Alignment Search Tool; BLASTP, Protein BLAST; CAMP, Collection of Antimicrobial Peptides; CSαβ, Cysteine stabilised α-helix and β-sheet fold peptides; Cys, Cysteine; DBAASP, Database of Antimicrobial Activity and Structure of Peptides; DRAMP, Data Repository of Antimicrobial Peptides; GO, Gene Ontogeny; GREP, Globally search a Regular Expression and Print; HMM, Hidden Markov Model; iAMPpred, Improved Prediction of Antimicrobial Peptides; InverPep, Invertebrate Antimicrobial Peptide Database; NCBI, National Center for Biotechnology Information; nr, Non-redundant protein sequence database; TBLASTN, Translated Nucleotide BLAST; WBPS, WormBase Parasite; WoS, Web of Science; YADAMP, Yet Another Database of Antimicrobial Peptides.