Computational protocol: Molecular characterization and functional analysis of a piscidin gene in large yellow croaker (Larimichthys crocea)

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Protocol publication

[…] Gene sequences used for multiple alignment and phylogenetic analysis are listed in . The similarity between the obtained sequences with other known sequences was analyzed using BLAST search (http://blast.ncbi.nlm.nih.gov/Blast.cgi). The cleavage site of signal peptides was predicted by the SignalP4.1 program (http://www.cbs.dtu.dk/services/SignalP/). Protein analysis was performed using online software on the ExPASy Server (http://www.expasy.org/tools/). Multiple sequence alignment was analyzed using the ClustalW program (http://clustalw.ddbj.nig.ac.jp/), and phylogenetic and molecular evolutionary analyses were conducted using MEGA version 5.0 (). […]

Pipeline specifications

Software tools SignalP, Clustal W, MEGA
Databases DDBJ ExPASy
Application Phylogenetics
Organisms Larimichthys crocea, Danio rerio, Vibrio alginolyticus, Escherichia coli, Aeromonas hydrophila, Vibrio anguillarum, Vibrio parahaemolyticus, Staphylococcus aureus, Listeria monocytogenes, Bacteria
Diseases Neoplasms
Chemicals Amino Acids