Computational protocol: Inducible ASABF-Type Antimicrobial Peptide from the Sponge Suberites domuncula: Microbicidal and Hemolytic Activity in Vitro and Toxic Effect on Molluscs in Vivo†

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Protocol publication

[…] Homology searches were conducted through servers at the European Bioinformatics Institute, Hinxton, United Kingdom and the National Center for Biotechnology Information (NCBI), Bethesda, MD []. Multiple alignments were carried out with ClustalW version 1.6 []. Phylogenetic trees were constructed on the basis of aa sequence alignments applying the Neighbor-Joining method to distance matrices that were calculated using the Dayhoff PAM matrix model [,]. The degree of support for internal branches was further assessed by bootstrapping []. The graphical output of the bootstrap figures was produced through the “Treeview” software [] and GeneDoc []. Potential domains, subunits, patterns, and transmembrane regions were predicted searching the Pfam [] or the SMART database []. […]

Pipeline specifications

Software tools Clustal W, TreeViewX
Databases Pfam
Application Phylogenetics
Organisms Suberites domuncula, Caenorhabditis elegans, Homo sapiens
Chemicals 2,2'-Dipyridyl, Quinolinic Acid