Computational protocol: Agr genes, missing in amniotes, are involved in the body appendages regeneration in frog tadpoles

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Protocol publication

[…] A translated BLAST program (tblast) was used to screen the available on-line nucleotide databases (all GeneBank: http://blast.ncbi.nlm.nih.gov/Blast.cgi; Ensembl: http://www.ensembl.org/index.html and A. mexicanum transcriptome: http://www.ambystoma.org) for sequences encoding proteins homologous to previously described Agr and TLP19 family proteins. The affiliation of each given gene to one of three syntenic loci (Ag1, Ag2/Agr3 or TLP19) was checked manually by comparing the genomic environment of a given gene, revealed by BLASTing the gene on the Ensembl database, with the genetic environment characteristic for each of the loci (Ag1, Ag2/Agr3 or TLP19). Multiple alignments and building of an unrooted phylogenetic tree with branch length were performed by using the standard CLUSTALW algorithm with the on-line program: http://www.genome.jp/tools/clustalw/. […]

Pipeline specifications

Software tools TBLASTN, Clustal W
Applications Phylogenetics, Amino acid sequence alignment
Organisms Xenopus laevis