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SON_SRRM2_speckles/README.md

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Description:

Analysis of SRRM2, SON, PRPF8, SRRM1, RBM25, Pinin and Coilin orthologues

Contents:

  • data - generally data files
    • genbank - primary sequence dataset in genbank format
    • genbank_final - final sequence dataset in genbank format
    • mobiDB - fasta sequence datasets and MobiDB-Lite results
    • NCBI_ortholog - vertebrate orthologues lists in .csv from NCBI ortholog resource
    • orthofinder - list of accession numbers for additional species obtained through Orthofinder2 analysis
  • results - results in tabular format
  • fig - figures

Notebooks:

  • Data_preparation.ipynb : dataset preparation and length comparison. Vertebrate SRRM2, SON, PRPF8, SRRM1, RBM25, Pinin and Coilin orthologous protein datasets were downloaded from NCBI’s orthologs and supplemented with orthologues predicted for invertebrate species using OrthoFinder. To visualize the results, protein lengths in each dataset were plotted on swarmplot.

  • Disorder_prediction.ipynb : Disorder prediction using IUPred2a and MobiDB-Lite. Visualized using Matplotlib's heatmap in two variants: sorted by phylogeny (TimeTree) and sorted by protein length.