https://github.com/applicativesystem/miniprot-analyzer

miniprot protein analyzer
https://github.com/applicativesystem/miniprot-analyzer

bioinformatics genome-analysis genome-annotation protein-alignment protein-alignments protein-sequences

Last synced: 7 days ago
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miniprot protein analyzer

• Host: GitHub
• URL: https://github.com/applicativesystem/miniprot-analyzer
• Owner: applicativesystem
• License: mit
• Created: 2024-08-17T19:02:10.000Z (4 months ago)
• Default Branch: main
• Last Pushed: 2024-08-17T19:04:46.000Z (4 months ago)
• Last Synced: 2024-11-10T20:18:13.544Z (about 1 month ago)
• Topics: bioinformatics, genome-analysis, genome-annotation, protein-alignment, protein-alignments, protein-sequences
• Language: Python
• Homepage:
• Size: 3.91 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# miniprot-protein-alignments

- a miniprot alignments to get the alignment ranges for the protein alignments that were done to generate the hints.

- generate the tabulated table for the length preparation. 

- Run the miniprot as the following. The function below ill map the length so that you can map the aligned length to the plotter. 

```

./miniprot --gff test/DPP3-hs.gen.fa.gz test/DPP3-mm.pep.fa.gz > aln.gff 

miniprotalignment("/home/gaurav/Desktop/aln.gff", splicetype="mRNA")

mRNA = miniprotalignment("/home/gaurav/Desktop/aln.gff", splicetype="mRNA")

length = [i[1]int(i[1][1]) - int(i[1][0]) for i in mRNA]

sns.plot(length) 

```

Gaurav Sablok \

University of Potsdam \

Potsdam,Germany