Computational protocol: Identification of Thyroid Hormones and Functional Characterization of Thyroid Hormone Receptor in the Pacific Oyster Crassostrea gigas Provide Insight into Evolution of the Thyroid Hormone System

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Protocol publication

[…] Sequence analysis was conducted using known invertebrate TRs and representative vertebrate TRs. The DNA-binding domain (DBD) and ligand-binding domain (LBD) sequences of TRs, determined using the Pfam web services (http://pfam.xfam.org/) [], were extracted and used to construct phylogenetic trees. Multiple alignments were performed with ClustalW [] and phylogenetic trees were constructed using four different algorithms (i.e., the maximum likelihood, maximum parsimony, neighbor-joining, and minimum-evolution) in MEGA5.0 software (http://www.megasoftware.net) []. Support values of the phylogenetic trees were derived by bootstrapping with 1000 replicates. […]

Pipeline specifications

Software tools Clustal W, MEGA
Databases Pfam
Application Phylogenetics
Organisms Crassostrea gigas, Caenorhabditis elegans
Chemicals Thyroid Hormones, Thyroxine, Triiodothyronine, Reverse