Computational protocol: Selective Blockade of Trypanosomatid Protein Synthesis by a Recombinant Antibody Anti-Trypanosoma cruzi P2β Protein

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Protocol publication

[…] Ribosomal P protein sequences of Trypanosoma cruzi, Saccharomyces cerevisiae and Homo sapiens were used to perform BLAST searches against NCBI-GenBank and GeneDB databases, using the tblastn and blastp algorithms. All protein sequences used for the phylogenetic analysis are listed in . Sequences were aligned with MEGA 4.0 software using the Clustal W algorithm with the PAM protein weight matrix, and all parameters with default settings. A phylogenetic tree was modeled using the minimum evolution method with the pairwise deletion option, and all parameters with default settings. Support for the branching order was determined by 1,000 bootstrap replicates. […]

Pipeline specifications

Software tools TBLASTN, BLASTP, MEGA, Clustal W
Databases GeneDB
Applications Phylogenetics, Amino acid sequence alignment
Organisms Trypanosoma cruzi, Homo sapiens, Rattus norvegicus, Trypanosoma brucei