Computational protocol: Involvement of Antizyme Characterized from the Small Abalone Haliotis diversicolor in Gonadal Development

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[…] The ORFs in the complete mRNA sequence of HdiODCAZ were identified using an ORF finder (http://www.ncbi.nlm.nih.gov/projects/gorf/orfig.cgi), and then the nucleotide sequences were translated into amino acids using the Vector NTI 11 software. The AZ sequence was analyzed using the ODC AZ finder software [], and the codon region and frameshifting site were identified.Homology searches were performed using BLASTn and BLASTp in NCBI. The Conserved Domain (CD) Search service was used to identify the CDs in the predicted protein sequences (http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml). 3-D structure of the predicted protein were predicted according to the methods described in the website http://bioinf.cs.ucl.ac.uk/psipred/. The deduced amino acid sequence of HdiODCAZ was aligned using the CLC main workbench software (http://www.clcbio.com) with the known homologous proteins of the AZ class obtained from GenBank. A phylogenetic tree was reconstructed using the CLC main workbench software through the neighbor-joining method for the amino acid sequences of AZs from the SwissProt databank/Genbank: red jungle fowl, Gallus gallus (O42148); human, Homo sapiens (P11926); house mouse, Mus musculus (P54369); Norway rat, Rattus norvegicus (P09057); pig, Sus scrofa (NP_001116466); cattle, Bos taurus (P27117); fruit fly, Drosophila melanogaster (P54361); mosquito, Aedes aegypti (Q95P51); red flour beetle, Tribolium castaneum (NP_001242998); yeast, Schizosaccharomyces pombe (Q9USQ5); sea purse, Triplophysa marmorata (AAG16236); zebrafish, Danio rerio (Q9YI97, Q9YI98); Atlantic salmon, Salmo salar (NP_001134904); African clawed frog, Xenopus laevis (P55814); zebra finch, Taeniopygia guttata (NP_001166235); and small abalone (ACV32415). […]

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