Computational protocol: Genome-Wide Identification, Characterization and Phylogenetic Analysis of ATP-Binding Cassette (ABC) Transporter Genes in Common Carp (Cyprinus carpio)

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Protocol publication

[…] Phylogenetic analysis can be used to support gene annotations, especially for non-model species. Reference ABC transporter genes from representative vertebrate model species were used for phylogenetic analysis, including Homo sapiens (human), Mus musculus (mouse), Gallus gallus (chicken), Xenopus tropicalis (frog), Oryzias latipes (medaka), and Danio rerio (zebrafish) for the phylogenetic analyses. The amino acid sequences were aligned using ClustalW (http://www.clustal.org/clustal2) with the default parameters. Several neighbor-joining phylogenetic trees were constructed using Clustal Omega (http://www.ebi.ac.uk/Tools/msa/clustalo/) with default settings of Pairwise Alignment and Multiple Sequence Alignment. Each common carp ABC protein was assigned to a family based on the phylogenetic analysis with the human and zebrafish ABC protein sequences. Separate phylogenetic trees were constructed for each ABC subfamily using the same methodology with other representative vertebrate species. […]

Pipeline specifications

Software tools Clustal W, Clustal Omega
Application Phylogenetics
Organisms Cyprinus carpio