Computational protocol: Endoplasmic Reticulum Stress–Related Genes in Yellow Catfish Pelteobagrus fulvidraco: Molecular Characterization, Tissue Expression, and Expression Responses to Dietary Copper Deficiency and Excess

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Protocol publication

[…] The core fragment, 3′ end and 5′ end sequences were assembled using SeqMan II software in DNASTAR PACKAGE to obtain full-length grp78, crt, perk, ire-1α, and atf-6α cDNAs. The sequences were edited and analyzed using the program EDITSEQ of DNASTAR package to search for the open reading frame (ORF) and then translated into amino acid sequences using standard genetic codes. The nucleotide sequences were compared with DNA sequences present in the GenBank database using BLAST network service at the NCBI (http://blast.ncbi.nlm.nih.gov/). Sequence alignments and percentage of amino acid conservation were assessed with the Clustal-W multiple alignment algorithm. For phylogenetic analysis, multiple sequence alignments were made with MAFFT () using an amino acid model at the GUIDANCE web server (http://guidance.tau.ac.il/) (), which pruned unreliably aligned regions by rejecting columns with confidence scores below 0.93. The phylogenetic tree was constructed with MEGA 5.0 () by the neighbor-joining (NJ) method based on the JTT+G model (), the best-fit model of sequence evolution obtained by ML model selection. The confidence of each node was assessed by 1000 bootstrap replicates. […]

Pipeline specifications

Software tools Clustal W, MAFFT, MEGA
Application Phylogenetics
Organisms Tachysurus fulvidraco
Diseases Deficiency Diseases
Chemicals Amino Acids, Glucose, Inositol