https://github.com/moshi4/pygenomeviz-data

pyGenomeViz data repository
https://github.com/moshi4/pygenomeviz-data

Last synced: 11 days ago
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pyGenomeViz data repository

• Host: GitHub
• URL: https://github.com/moshi4/pygenomeviz-data
• Owner: moshi4
• Created: 2022-06-06T12:41:17.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2022-10-26T15:37:21.000Z (about 2 years ago)
• Last Synced: 2023-03-05T20:26:36.482Z (over 1 year ago)
• Size: 18.7 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# pygenomeviz-data

Dataset repository for [pyGenomeViz](https://github.com/moshi4/pyGenomeViz) examples.

## Resources

### Genbank Dataset

- ***Escherichia phage*** (`escherichia_phage`)  

  Four *Escherichia phage* genome dataset (max_genome_size=72,179 bp).  

  It contains protein sequence similarity comparison links generated by MUMmer.

  - JX128258

  - MH051335

  - MK373776

  - MH816966

- ***Erwinia phage*** (`erwinia_phage`)  

  Four *Erwinia phage* genome dataset (max_genome_size=358,115 bp).  

  It contains protein sequence similarity comparison links generated by MUMmer.

  - MT939746

  - MT939487

  - MT939488

  - LT96552

- ***Enterobacteria phage*** (`enterobacteria_phage`)  

  Six *Enterobacteria phage* genome dataset (max_genome_size=45,206 bp).  

  It contains CDS similarity comparison links generated by MMseqs.

  - NC_019724

  - NC_024783

  - NC_016566

  - NC_013600

  - NC_031081

  - NC_028901

  

- ***Escherichia coli*** (`escherichia_coil`)  

  Four *E.coli* genome dataset (max_genome_size=5,498,450 bp).  

  It contains nucleotide sequence similarity comparison links generated by MUMmer.

  - NC_000913

  - NC_002695

  - NC_011751

  - NC_011750

- ***Mycoplasma gallisepticum*** (`mycoplasma_gallisepticum`)  

  Six `M.gallisepticum` genome dataset (max_genome_size=1,012,800 bp).  

  It contains CDS similarity comparison links generated by MMseqs.  

  - NC_004829

  - NC_018407

  - NC_018408

  - NC_018409

  - NC_017502

  - NC_017503

### GFF Files

- **enterobacteria_phage.gff** (genome_size=60,942 bp)  

  RefSeq assembly accession: [GCF_000844925.1](https://www.ncbi.nlm.nih.gov/assembly/GCF_000844925.1/)  

- **escherichia_coli.gff.gz** (genome_size=4,641,652 bp)  

  RefSeq assembly accession: [GCF_000005845.2](https://www.ncbi.nlm.nih.gov/assembly/GCF_000005845.2)