Computational protocol: Early Embryonic Expression of a Putative Ecdysteroid-Phosphate Phosphatase in the Water Flea,Daphnia magna(Cladocera: Daphniidae)

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Protocol publication

[…] A multiple sequence alignment was constructed using Clustal-W ( ) with the following settings for the pairwise alignment parameters: gap opening penalty, 17.00; gap extension penalty, 0.1; and the identity protein weight matrix. The multiple alignment parameters were as follows: gap opening penalty, 17.00; gap extension penalty, 0.2; delay divergent cutoff, 30%; and gap separation distance, 4. The phylogenetic reconstruction was performed using the p-distance algorithm and the neighbor-joining method implemented in MEGA software version 5.05 ( ). The known orthologs of EPPase and the sequences that showed high similarity were used to construct a phylogenetic tree. A BLAST search was conducted on the D. pulex EST-genome database for sequences related to EPPase in the D. pulex ( ). The amino acid sequence corresponding to the EPPase histidine phosphatase domain was used for the analysis. […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics
Organisms Daphnia magna, Homo sapiens
Chemicals Ecdysteroids