Computational protocol: Anopheles aquasalis Infected by Plasmodium vivax Displays Unique Gene Expression Profiles when Compared to Other Malaria Vectors and Plasmodia

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Protocol publication

[…] The sequences obtained were submitted to the STINGRAY platform (System for Integrated Genomic Resources and Analyses) (http://stingray.biowebdb.org/). Vector and primer sequences were trimmed and quality evaluated by Phred, Phrap and Consed programs. The sequences were clustered using the CAP3 program and clusters were searched for similarity using the BLASTN and BLASTX algorithm with sequences of insects, plasmodia and different databases (RefSeq, UniRef, UniProt, InterProt, KOG, COG, Prk, Smart and CDD). The cutoff e-values utilized were ≥10-5 for tBLASTX similarity and 10-10 for BLASTN. Sequences were annotated and grouped in functions. Nucleotide sequences have been submitted to Genbank and their respective accession numbers are indicated in , , , . [...] The sequences were aligned using the ClustalW (http://www.ebi.ac.uk/Tools/clustalw2/) and presented with BOXSHADE (http://bioweb.pasteur.fr/seqanal/interfaces/boxshade.html) programs. For phylogenetic analyses, the sequence alignments were examined with the Mega program (Molecular Evolutionary Genetics analysis, version 4) . Relationships between the sequences were assessed by neighbor-joining method with amino acid distances with 1,000 replications in the bootstrap test. […]

Pipeline specifications

Software tools BLASTN, BLASTX, TBLASTX, Clustal W, BoxShade, MEGA
Databases UniRef
Applications Phylogenetics, Nucleotide sequence alignment, Proteome data visualization
Organisms Plasmodium vivax, Homo sapiens
Diseases Infection, Malaria