ParaDB: a manually curated database for the human pathogenic fungi Paracoccidioides spp.
The genus Paracoccidioides consists of thermodymorphic fungi responsible for Paracoccidioidomycosis (PCM), a systemic mycosis that has been registered to affect ~10 million people in Latin America. Currently, the genus is subdivided into five different species, each represented by a reference isolate: P. lutzi (represented by isolate Pb01), P. brasiliensis (represented by isolate Pb18), P. americana (represented by isolate Pb03), P. restrepiensis (represented by isolate PbCnh) and P. venezuelensis (represented by isolate Pb300). Although genomic sequencing has already been obtained for all these five Paracoccidioides isolates, functional annotations of these genomes, available in central databases such as NCBI/RefSeq or Ensembl, have not been submitted to manual curation and, as a result, ~60-90% of the Paracoccidioides protein-coding genes (depending on isolate/annotation) are currently described as responsible for hypothetical proteins, without any further functional/structural description. ParaDB provides revised annotations for these isolates, based on extensive manual curation, which reduced the number of hypothetical proteins in their genomes to ~25 – 28%. This site also provides researches with resources to facilitate data mining of Paracoccidioides genomes, including search tools based on keywords or protein/DNA sequences.
All data contained in ParaDB can be partially or completely downloaded through spreadsheet, multi-fasta and GFF3-formatted files, which can be subsequently used in a variety of downstream functional analyses, aiding researchers in this field to conduct post-genomic studies with this important group of human pathogenic fungi.