Computational protocol: Molecular Detection of Bioluminescent Dinoflagellates in Surface Waters of the Patagonian Shelf during Early Austral Summer 2008

Similar protocols

Protocol publication

[…] The sequences obtained from the clones of the lcf PCR products were trimmed of vector and primers and their identity was confirmed using the BLASTn tool of the NCBI database (http://blast.ncbi.nlm.nih.gov/Blast.cgi). All further sequence analyses were conducted in the MEGA v. 5 software . New sequences were aligned to those of cultured representatives obtained from GenBank that had been split into the three repeated domains that comprise the lcf in photosynthetic species. Alignments were carried out using ClustalW and improved manually. A genetic distance (p-distance) matrix was generated to compare the similarities of environmental lcf sequences to those of cultured isolates. Sequences of different lengths were compared by discarding gaps only in pairwise comparisons. The distance matrix was visualized as a dendrogram constructed using the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) algorithm and statistically assessed with 1000 bootstrap replications. […]

Pipeline specifications

Software tools BLASTN, MEGA-V, Clustal W
Application GWAS