Computational protocol: Identification, visualization and clonal analysis of intestinal stem cells in fish

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Protocol publication

[…] Sequences of various vertebrate LGR proteins were retrieved from NCBI: Danio rerio LGR4 (accession no. E7FE13), Danio rerio LGR6 (P0DM44), Human LGR4 (AAH33039), Human LGR5 (AAH96325), Human LGR6 (AAH47905), Human LGR7 (AAG17167), mouse LGR4 (NP_766259), mouse LGR5 (NP_034325), mouse LGR6 (NP_001028581), Oryzias latipes LGR4 (BAM29306), Oryzias latipes LGR5 (predicted, XP_004085697), Oryzias latipes LGR6 (BAM29305), Xenopus laevis LGR5a (ADK66918) and Xenopus laevis LGR5b (ADZ55458). BLAST at the ENSEMBL (http://www.ensembl.org/info/about/species.html) confirmed identity of medaka lgr5 (Oryzias latipes, scaffold2947: 4002-5617). Alignments were created with ClustalW and phylogenetic relationships were deduced after alignment of protein sequences with Geneious (v.8.1.6) following a neighbour-joining approach. […]

Pipeline specifications

Software tools Clustal W, Geneious
Application Phylogenetics