Computational protocol: PmRunt regulated by Pm-miR-183 participates in nacre formation possibly through promoting the expression of collagen VI-like and Nacrein in pearl oyster Pinctada martensii

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Protocol publication

[…] Similarity analysis of protein sequence was conducted using the BLAST program from the US National Center for Biotechnology Information (http://blast.ncbi.nlm.nih.gov/Blast.cgi). The deduced amino acid sequence was analysed in Expert Protein Analysis System (http://www.expasy.org). The protein domain was predicted with the simple modular architecture research tool version 5.1 (http://www.smart.emblheidelberg.de/). The multiple alignment of the deduced amino acid sequence of PmRunt or PmCBFβs with other species was performed using the ClustalW multiple alignment program (http://www.ebi.ac.uk/clustalw/). The phylogenetic tree of PmRunt and other species was constructed in Mega 6.0. The sequence accession numbers are listed in . Target prediction between Pm-miR-183 and PmRunt was performed using the miRanda and microTar software packages. The same interaction positions were selected as potential target sites. We submitted the PmRunt and CBF sequences, which would be used to construct 3D models, through Phyre2 (http://www.sbg.bio.ic.ac.uk/phyre2/protocol) []. Chimera 1.8.1 was used to display these models. […]

Pipeline specifications

Software tools Clustal W, MicroTar, Phyre
Databases SMART ExPASy
Application Phylogenetics