Computational protocol: Zebrafish RNase T2 genes and the evolution of secretory ribonucleases in animals

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Protocol publication

[…] Identification of RNase T2 genes was done by BLAST searches in the zebrafish (Danio rerio) genome (version Zv7, available through the National Center for Biotechnology Information (NCBI), . Analyses of the medaka (Oryzias latipes), spotted green pufferfish (Tetraodon nigroviridis), and other full genomes was also performed using NCBI resources. Analysis of the fugu (Takifugu rubripes) genome was performed using Assembly Release 4 from the Fugu BLAST server . Expressed sequence tag (EST) sequences and protein sequences were also obtained by BLAST searches of the NCBI EST-other and non-redundant databases respectively. Analysis of genome organization for the RNase Dre1 and RNase Dre2 genes was done using contigs obtained by combining information from cDNAs cloned by our laboratory (supplementary dataset) and ESTs obtained from NCBI EST-other.Prediction of signal peptides and subcellular localization was carried out using PSORT [], WoLF PSORT [] and SignalP and TargetP [].Arabidopsis microarray data were obtained from the Arabidopsis information Resource (TAIR) database. Mouse microarray data were obtained from the Genomics Institute of the Novartis Research Foundation SymAtlas . Nematode microarray data were obtained from WormBase . In all cases, normalized data were used, and values belonging to the same experiment set were compared. [...] Protein sequences were aligned using ClustalW2 [] followed by manual adjustments. PAUP 4.0 software [] was used for phylogenetic analyses. Phylogenetic trees were constructed using the Neighbor-Joining tree method [] with 1,000 bootstrap replications. […]

Pipeline specifications

Software tools PSORT, WoLF PSORT, SignalP, TargetP, Clustal W, PAUP*
Databases TAIR WormBase Symatlas
Applications Phylogenetics, Protein sequence analysis
Organisms Danio rerio