Computational protocol: Functional Analysis of atfA Gene to Stress Response in Pathogenic Thermal Dimorphic Fungus Penicillium marneffei

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Protocol publication

[…] The complete genomic sequence of the atfA gene was obtained by PCR amplification using the genomic DNA of P. marneffei strain F4 as the DNA template. Primers AtfA-WF and AtfA-WR () were designed based on the genome database of P. marneffei ATCC 18224 (whole genome shotgun sequencing project; http://www.ncbi.nlm.nih.gov). The 1677-bp amplicon was sequenced in both directions. The NCBI BLAST program (http://www.ncbi.nlm.nih.gov) was used to search for nucleotide and protein sequence similarities. The programs ‘nucleic acid translation’ of BioEdit Sequence Alignment Editor Software was used to predict an open reading frame and deduced amino acid sequences from the nucleotide sequences. Conserved domains of AtfA putative protein were predicted using ScanProsite tool (http://prosite.expasy.org/scanprosite/). Deduced amino acid sequences of the atfA genes of other fungal homologous sequences that were obtained from GenBank databases (http://www.ncbi.nlm.nih.gov) were used for multiple alignments. Multiple sequence alignment was generated with the ClustalW program (http://www. ebi.ac.uk/clustalw/index.html). […]

Pipeline specifications

Software tools BLASTN, BioEdit, ScanProsite, Clustal W
Databases PROSITE ExPASy
Application Protein sequence analysis
Organisms Mus musculus, Talaromyces marneffei, Homo sapiens
Diseases Infection, HIV Infections, Mastocytosis, Systemic
Chemicals Amphotericin B, Hydrogen Peroxide, Sorbitol, Itraconazole, tert-Butylhydroperoxide, Vitamin K 3