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This code is associated with the paper from Fallon et al., "Firefly genomes illuminate parallel origins of bioluminescence in beetles". eLife, 2018.

This is a Python3 script which is designed to take a Uniprot reference proteome in FASTA format (which are non-redundant in peptide sequence, but may have multiple isoforms per gene), and attempt to filter down the protemome to a single "canonical isoform" per gene.

If your organism is already well-manually reviewed on Uniprot (e.g. the protein is included in the SwissProt database), it has already undergone such reduction to a single canonical isoform per gene (barring some exceptions where the definition of "gene" gets a bit tricky).

This "well-manually reviewed" criteria really only holds true for human, budding-yeast, Arabidopsis thaliana, and E. coli. Everything else (e.g. D. melanogaster) is "barely" manually reviewed, and this script can help reduce redundancy.

The script filters on three criteria:

  1. Is there a single manually-reviewed SwissProt protein per gene-isoform cluster? If so, pass only that protein, and do not pass the rest. If there is >1, then it is reported as a "special-case", and all proteins in that gene-cluster are passed. If it is 0, then that gene-cluster goes into the next steps for further evaluation/
  2. Filter based on the Uniprot protein existence annotation. If there is 1 isoform that has a better protein existence than all the others in the gene-isoform cluster, then it is passed, and the rest are not passed. If there is >1 proteins that are equal in terms of their existence annotation, then put those proteins into the 3rd step.
  3. Pass the isoform which has the greatest bitscore, when BLASTPed to the proteomes (non-redundant, non filtered) of closely related species. If the isoform BLASTP bitscores are tied, pass all isoforms. If the isoforms don't BLASTP to anything, they will all have the same bitscore, and they will all get passed.

See the examples folder for more details.

Peptides which pass these filters are output on the stdout. All other information is output on stderr.

Representative results are below:


  • Drosophila melanogaster (unfiltered)

    • 21,957 proteins (for 14,213 protein coding genes)
    • BUSCO score: C:99.8%[S:67.0%,D:32.8%],F:0.2%,M:0.0%,n:2442
    • Checksum: 4c3a21d508b6186df11b4ff0e256dbf9
  • Drosophila melanogaster (script filtered)

    • 15,152 proteins (for 14,213 protein coding genes)
    • BUSCO score: C:99.5%[S:92.7%,D:6.8%],F:0.3%,M:0.2%,n:2442
    • Checksum: a658be4b7b7cd3dc9f06b5a913756c9e
  • Tribolium castaneum (unfiltered)

    • 18,505 proteins (for 16,578 protein coding genes)
    • BUSCO score: C:98.1%[S:89.4%,D:8.7%],F:1.5%,M:0.4%,n:2442
  • Tribolium castaneum (script filtered)

    • 16,991 proteins (for 16,578 protein coding genes)
    • BUSCO score: C:98.0%[S:95.8%,D:2.2%],F:1.6%,M:0.4%,n:2442
    • Checksum: 911e0fe07450b7dc64e384995dd73252


A Python3 script to reduce gene-isoform redundancy in Uniprot reference proteome files




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