PMID- 31306428
OWN - NLM
STAT- MEDLINE
DCOM- 20200106
LR  - 20231013
IS  - 1935-2735 (Electronic)
IS  - 1935-2727 (Print)
IS  - 1935-2727 (Linking)
VI  - 13
IP  - 7
DP  - 2019 Jul
TI  - ParaDB: A manually curated database containing genomic annotation for the human 
      pathogenic fungi Paracoccidioides spp.
PG  - e0007576
LID - 10.1371/journal.pntd.0007576 [doi]
LID - e0007576
AB  - BACKGROUND: 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. Biogeographical data 
      subdivided the genus Paracoccidioides in five divergent subgroups, which have 
      been recently classified as different species. Genomic sequencing of five 
      Paracoccidioides isolates, representing each of these subgroups/species provided 
      an important framework for the development of post-genomic studies with these 
      fungi. However, functional annotations of these genomes 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. PRINCIPAL FINDINGS: The present work reviews the functional 
      assignment of Paracoccidioides genes, reducing the number of hypothetical 
      proteins to ~25-28%. These results were compiled in a relational database called 
      ParaDB, dedicated to the main representatives of Paracoccidioides spp. ParaDB can 
      be accessed through a friendly graphical interface, which offers 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. Moreover, the entire ParaDB environment has been configured 
      in a Docker service, which has been submitted to the GitHub repository, ensuring 
      long-term data availability to researchers. This service can be downloaded and 
      used to perform fully functional local installations of the database in 
      alternative computing ecosystems, allowing users to conduct their data mining and 
      analyses in a personal and stable working environment. CONCLUSIONS: These new 
      annotations greatly reduce the number of genes identified solely as hypothetical 
      proteins and are integrated into a dedicated database, providing resources to 
      assist researchers in this field to conduct post-genomic studies with this group 
      of human pathogenic fungi.
FAU - Aciole Barbosa, David
AU  - Aciole Barbosa D
AUID- ORCID: 0000-0003-3875-2307
AD  - Nucleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes (UMC), Mogi 
      das Cruzes, Sao Paulo, Brazil.
FAU - Menegidio, Fabiano Bezerra
AU  - Menegidio FB
AD  - Nucleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes (UMC), Mogi 
      das Cruzes, Sao Paulo, Brazil.
FAU - Alencar, Valquiria Campos
AU  - Alencar VC
AD  - Nucleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes (UMC), Mogi 
      das Cruzes, Sao Paulo, Brazil.
FAU - Goncalves, Rafael S
AU  - Goncalves RS
AD  - Nucleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes (UMC), Mogi 
      das Cruzes, Sao Paulo, Brazil.
FAU - Silva, Juliana de Fatima Santos
AU  - Silva JFS
AD  - Nucleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes (UMC), Mogi 
      das Cruzes, Sao Paulo, Brazil.
FAU - Vilas Boas, Renata Ozelami
AU  - Vilas Boas RO
AD  - Nucleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes (UMC), Mogi 
      das Cruzes, Sao Paulo, Brazil.
FAU - Faustino de Maria, Yara Natercia Lima
AU  - Faustino de Maria YNL
AD  - Nucleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes (UMC), Mogi 
      das Cruzes, Sao Paulo, Brazil.
FAU - Jabes, Daniela Leite
AU  - Jabes DL
AUID- ORCID: 0000-0001-7297-0784
AD  - Nucleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes (UMC), Mogi 
      das Cruzes, Sao Paulo, Brazil.
FAU - Costa de Oliveira, Regina
AU  - Costa de Oliveira R
AD  - Nucleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes (UMC), Mogi 
      das Cruzes, Sao Paulo, Brazil.
FAU - Nunes, Luiz R
AU  - Nunes LR
AUID- ORCID: 0000-0001-9619-269X
AD  - Centro de Ciencias Naturais e Humanas, Universidade Federal do ABC (UFABC), Sao 
      Bernardo do Campo, Sao Paulo, Brazil.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20190715
PL  - United States
TA  - PLoS Negl Trop Dis
JT  - PLoS neglected tropical diseases
JID - 101291488
RN  - 0 (Fungal Proteins)
SB  - IM
MH  - Amino Acid Sequence
MH  - Base Sequence
MH  - Computers, Molecular
MH  - *Databases, Genetic
MH  - Ecosystem
MH  - Fungal Proteins/genetics
MH  - Genome, Fungal/*genetics
MH  - Humans
MH  - Latin America
MH  - *Molecular Sequence Annotation
MH  - Paracoccidioides/*genetics/isolation & purification
MH  - Paracoccidioidomycosis/*microbiology
MH  - Research
PMC - PMC6658007
COIS- The authors have declared that no competing interests exist.
EDAT- 2019/07/16 06:00
MHDA- 2020/01/07 06:00
PMCR- 2019/07/15
CRDT- 2019/07/16 06:00
PHST- 2019/01/17 00:00 [received]
PHST- 2019/06/24 00:00 [accepted]
PHST- 2019/07/25 00:00 [revised]
PHST- 2019/07/16 06:00 [pubmed]
PHST- 2020/01/07 06:00 [medline]
PHST- 2019/07/16 06:00 [entrez]
PHST- 2019/07/15 00:00 [pmc-release]
AID - PNTD-D-19-00082 [pii]
AID - 10.1371/journal.pntd.0007576 [doi]
PST - epublish
SO  - PLoS Negl Trop Dis. 2019 Jul 15;13(7):e0007576. doi: 
      10.1371/journal.pntd.0007576. eCollection 2019 Jul.