Computational protocol: Molecular, Cellular and Physiological Evidences for the Anorexigenic Actions of Nesfatin-1 in Goldfish

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Protocol publication

[…] NUCB2 gene/mRNA and protein sequencing information for zebrafish (Danio rerio), Western clawed frog (Xenopus tropicalis), chicken (Gallus gallus), mouse (Mus musculus) and human (Homo sapiens) were obtained from annotated sequences available through the GenBank (http://www.ncbi.nlm.nih.gov/genbank/) and the Ensembl genome databases (http://www.ensembl.org/index.html). With the exception of zebrafish, all other teleost NUCB2 sequences have not yet been annotated. In addition, two paralogous zebrafish NUCB2 genes, NUCB2A and NUCB2B, exist due to the teleost-specific whole-genome duplication. We compiled all other teleost NUCB2 sequences from the Ensembl genome databases using the zebrafish NUCB2A and NUCB2B protein sequences as the in silico probes. We aligned similar sequences which most highly match with those two paralogous NUCB2 in zebrafish within the genomes of stickleback (Gasterosteus aculeatus), medaka (Oryzias latipes), green pufferfish (Tetraodon nigroviridis) and fugu (Takifugu rubripes). In addition, NUCB1 sequences were available for many species within Genbank and Ensembl databases. The NUCB1 and NUCB2 sequences obtained were aligned using ClustalW2 general purpose multiple sequence alignment program for DNA or protein . A phylogenetic analysis based on the amino acid sequences was constructed using the freeware “Phylogeny.fr” (http://www.phylogeny.fr/) . […]

Pipeline specifications

Software tools Clustal W, Phylogeny.fr
Application Phylogenetics
Organisms Carassius auratus, Homo sapiens, Danio rerio
Diseases Hypothalamic Neoplasms