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

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

bioinformatics genome-alignment genome-analysis genome-annotation genome-bioinformatics genome-informatics protein-alignment

Last synced: 7 days ago
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miniprot protein alignment analyzer

• Host: GitHub
• URL: https://github.com/applicativesystem/miniprot-protein-annotator
• Owner: applicativesystem
• License: mit
• Created: 2024-08-17T18:58:37.000Z (4 months ago)
• Default Branch: main
• Last Pushed: 2024-08-17T19:00:33.000Z (4 months ago)
• Last Synced: 2024-11-10T20:18:13.592Z (about 1 month ago)
• Topics: bioinformatics, genome-alignment, genome-analysis, genome-annotation, genome-bioinformatics, genome-informatics, protein-alignment
• Language: Python
• Homepage:
• Size: 24.4 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# miniprot-protein-annotator

- a protein coding regions annotator that will take the alignment file in the PAF/GFF format and will generate the fasta from the corresponding fasta files for the aligned regions.

- implemented faster rates so that you can parse as many aligned regions as you want.

- you can also create the protein tokenzier from the same for machine learning.

```

 # align your genome with the given protein  using the miniprot such as 

   miniprot --gff genome.fasta protein.fasta > sample.gf

```

 - and then run the proteinannotator to extract all the complete coding regions 

 ```

generatingAlignments("/home/gaurav/Desktop/final_code_push/multi.gff", 

                        "/home/gaurav/Desktop/final_code_push/multi.fasta", 

                               "/home/gaurav/Desktop/final_code_push/multiout.fasta")

```

Gaurav Sablok \

University of Potsdam \

Potsdam,Germany