Computational protocol: A Scallop Nitric Oxide Synthase (NOS) with Structure Similar to Neuronal NOS and Its Involvement in the Immune Defense

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Protocol publication

[…] The homology searches of the cDNA sequence and amino acid sequence of CfNOS were conducted with BLAST algorithm at the National Center for Biotechnology Information (http://www.ncbi.nlm.gov/blast). The deduced amino acid sequence was analyzed with the Expert Protein Analysis System (http://www.expasy.org). The presence and location of signal peptide was predicted using the SignalP 3.0 program (http://www.cbs.dtu.dk/services/SignalP). The protein domains were predicted with the simple modular architecture research tool (SMART) version 7.0 (http://www.smart.emblheidelberg.de/). The multiple sequence alignment of CfNOS with other NOSs was performed with the ClustalW multiple alignment program (http://www.ebi.ac.uk/clustalw/) and displayed through the multiple alignment show program (http://www.bio-soft.net/sms/index.html). An unrooted phylogenic tree was constructed based on the deduced amino acid sequence of CfNOS and other NOSs by the Maximum Likelihood (ML) algorithm using the Seaview 4.0 software [,]. […]

Pipeline specifications

Software tools SignalP, Clustal W, SeaView
Databases SMART ExPASy
Organisms Azumapecten farreri
Chemicals Nitric Oxide