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Protein coverage visualization #541

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henninggaertner opened this issue Nov 14, 2024 · 0 comments · May be fixed by #542
Open
5 tasks

Protein coverage visualization #541

henninggaertner opened this issue Nov 14, 2024 · 0 comments · May be fixed by #542
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@henninggaertner
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Issue description

This is a feature request.
It is useful to be able to visualize the coverage of proteins by the peptides measured during MS.
[ ] A FASTA file Wikipedia provides the protein sequences, an example can be downloaded from Uniprot. Support for importing that data format needs to be added.
[ ] The peptides can be imported into PROTzilla using the peptide / evidence import, although support for qualitative data could be needed to added, depending on the example data.
[ ] The peptide sequences then need to be aligned with the protein sequence, this can be solved with simple k-mer matching or maybe a non-trivial substring search algorithm like Aho-Corasick or Boyer-Moore.
[ ] Once the peptide's possible locations are known, a plot needs to be generated (Plotly), the specifics of which are TBD (@cschlaffner)

Acceptance Criteria

  • Fasta can be imported
  • The example data is supported
  • The peptide sequence matching is implemented
  • The plotting step exists (inputs: protein, peptide data)
  • Integration of all previous steps into one functional workflow
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