Computational protocol: Retroactive Maintains Cuticle Integrity by Promoting the Trafficking of Knickkopf into the Procuticle of Tribolium castaneum

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Protocol publication

[…] An extensive, genome-wide search for homologs of DmRtv in the T. castaneum genome database was performed using NCBI programs TBLASTN and BLASTP and using the amino acid sequence of DmRTV as query. [...] Rtv-like proteins were identified by TBLASTN searches of the fully sequenced genomes of T. castaneum, Anopheles gambiae, Aedes aegypti, Culex quinquefasciatus, Bombyx mori, Acyrthosiphon pisum, Nasonia vitripennis and Ixodes scapularis using the amino acid sequence of DmRtv as query. Multiple sequence alignments of TcRtv and the related Rtv-like proteins from other insects and arthropods were carried out using the ClustalW software prior to phylogenetic analysis. A consensus phylogenetic tree was constructed using MEGA 4.0 neighbor joining method . […]

Pipeline specifications

Software tools TBLASTN, BLASTP, Clustal W, MEGA
Applications Phylogenetics, Amino acid sequence alignment
Organisms Tribolium castaneum
Diseases Congenital Abnormalities