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Topic4_TeamA (Aquadocs)

AquaPathoPedia, a sequence database with analysis tools for marine microbial diseases

We created AquaPathoPedia, a sequence database for host-associated viral and bacterial pathogens in marine environments

AquaPathoPedia (aquapathopedia_dataset.tsv) contains data from:

  • 2,681 viral genome records
  • 542 bacterial genome records
  • 226 full-length bacterial 16S rRNA gene records

Data collection and curation pipeline is described here. All data (metadata, sequence data, and BLAST-formatted databaes) is available at DOI

Usage

AquaPathoPedia is useful for:

  • Bacterial/viral marine pathogen evolutionary/phylogenetic analysis
  • Analysis of host distribution of specific marine diseases
  • Sequence analysis of pathogenic signatures in marine hosts

Note:

  • Currently, the AquaPathoPedia web server http://10.119.34.34:8004/Ocean/ can only be accessed from University of South Florida's in-campus network
  • Users can clone this github repository or download website.zip from this repository to run the web server locally

Local installation requirements

  1. bash
  2. conda 4.7.12
  3. python 3.9.6
  4. django 2.2.5
  5. ncbi-blast-2.9.0+

Keyword search

  • Launch the server http://10.119.34.34:8004/Ocean/ or local server
  • Enter keywords such as 'Virus' or 'Bacteria'
  • A results page will show up once the search is completeted, click on 'download' to save the information

BLAST search against AquaPathoPedia (coming soon)

  • Upload sequence(s) in fasta or multi-fasta format
  • Sequence(s) will be searched against the database based on default BLAST parameters
  • Download and save results

Reference

If you use project AquaPathoPedia for your research, please cite:

*Manuscript in preparation