Computational protocol: Genetic Polymorphisms and Phenotypic Profiles of Sulfadiazine-Resistant and Sensitive Toxoplasma gondii Isolates Obtained from Newborns with Congenital Toxoplasmosis in Minas Gerais, Brazil

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Protocol publication

[…] The forward and reverse sequences obtained from each exon were processed using Phred and CAP3 []. Bases with a phred score lower than 20 were removed (PMID:9521922). Strain polymorphisms were analyzed by alignment of the contig sequences using the multiple sequence alignment program ClustalW (http://www.ebi.ac.uk/Tools/msa/clustalw2/). The sequences of the strains GT1 (type I), ME49 (type II), and VEG (type III) obtained from the ToxoDB database (http://www.toxodb.org) were used as reference. The protein sequences of each isolate were compared using tblastn (Translated BLAST, http://www.blast.ncbi.nlm.gov/) translated by ExPASy Tools Translate (http://www.expasy.org/tools/) and submitted to multiple alignments using ClustalW. […]

Pipeline specifications

Software tools CAP3, Clustal W, TBLASTN
Databases ToxoDB
Application Amino acid sequence alignment
Organisms Toxoplasma gondii, Homo sapiens, Mus musculus
Diseases Toxoplasmosis, Congenital, Leukemia, T-Cell
Chemicals Sulfadiazine, Sulfonamides