Describes environmental preferences of microbes, interactions with other organisms, biochemical phenotypes, resistance to chemicals and other stressors. ProTraits recognizes 424 phenotypic traits and covers 3,046 bacterial or archeal species. Overall, it provides 545,081 annotations (less than 10% of false discovery rate (FDR), tallying both the positive and the negative labels), of which 503,308 are novel. Moreover, the ProTraits pipeline can infer phenotypes using five independant sources of genomic data, while providing estimates of FDRs that agree with manual curation.

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ProTraits forum

No open topic.

ProTraits classification

  • Archaebacteria
  • Eubacteria
    • Bacillus subtilis
    • Escherichia coli
    • Mycobacterium tuberculosis
    • Mycoplasma pneumoniae
    • Helicobacter pylori
    • Staphylococcus aureus

ProTraits specifications

Restrictions to use:
None
Database management system:
MySQL
Data access:
File download, Web user interface
Source code URL:
http://protraits.irb.hr/data.html
Programming languages:
Java, Python, R
Community driven:
No
User data submission:
Not allowed

Publications

  • (Brbic et al., 2016) The landscape of microbial phenotypic traits and associated genes. Nucleic Acids Res.
    PMID: 27915291

ProTraits support

Documentation

Credits

Institution(s)

Division of Electronics, Ruder Boskovic Institute, Zagreb, Croatia; Mediterranean Institute of Life Sciences, Split, Croatia; EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain

Funding source(s)

This work was funded by the Croatian Science Foundation grants HRZZ-9623 (DescriptiveInduction) HRZZ- 5660 (MultiCaST), the European Union FP7 grants ICT-2013-612944 (MAESTRA), the REGPOT-2012-2013- 1-316289 (InnoMol), the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013-2017’ (SEV-2012- 0208) and the FP7 project 4DCellFate (277899).

Link to literature

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