Computational protocol: Identification and Expression Profiles of IL-8 in Bighead Carp (Aristichthys nobilis) in Response to Microcystin-LR

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Protocol publication

[…] Purified PCR products were ligated into pMD18-T vectors (TaKaRa), and three plasmids were sequenced for each product, respectively. Sequences were analyzed based on nucleotide and protein databases using the BLAST program (http://www.ncbi.nlm.nih.gov/BLAST/). The protein prediction was performed using software at the ExPASy Molecular Biology Server (http://expasy.pku.edu.cn). The protein family signature was identified by InterPro (http://www.ebi.ac.uk/interpro/). The chemokine CXC domain was defined by National Center for Biotechnology Information (NCBI) conserved-domain database (http://www.ncbi.nlm.nih.gov/structure). Multiple sequence alignment was performed using the CLUSTALW 2 program (http://clustalw.genome.jp/). Phylogenetic tree was constructed by using the neighbor-joining (NJ) method with 1000 bootstrap in the Mega 5 software package. […]

Pipeline specifications

Software tools InterPro, Clustal W, MEGA
Databases CDD ExPASy
Applications Phylogenetics, Protein sequence analysis
Organisms Hypophthalmichthys nobilis