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Supplementary material for "Evolution of sequence-diverse disordered regions in a protein family: order within the chaos"

dataset
posted on 19.03.2020 by Thomas Shafee, KIM JOHNSON, Tony Bacic

A set of supplementary data files

Accompanying publication: Evolution of sequence-diverse disordered regions in a protein family: order within the chaos


Supp data file 1

Excel file for the 2644 fasciclin domains, names and annotation information. In order to keep names short for phylogenies, FLAs given arbitrary identifier numbers, and fasciclin domains within them indicated by their (e.g. “>X1234_FLA.2.3” -> Fasciclin domain cluster 1, arbitrary FLA identifier number 1234, FLA fasciclin domain 2 out of 3). Numbers and colours given for fasciclin, AG, non-AG and inter-proline clusters.

Fields:

  • name = sequence name (constructed as: G[fas.clust] X[number] fas [fas.count] of [fas.max] ; also used in alignments and phylogenies).
  • number = Arbitrary ID number for the FLA sequence· Accession = Phytosome gene sequence ID for the FLA sequence
  • fas.count = Which fasciclin domain is this within the FLA sequence
  • fas.max = How many total fasciclin domains are in the FLA sequence
  • fas.clust(PCA) = Initial cluster based on PCA+MClust of fasciclin domain sequence
  • fas.clust = Cluster based on UMAP+HDBSCAN of fasciclin domain sequence (0=no cluster assigned, 1=type A, 2=type B, etc.)
  • agreg.clust = Cluster based on UMAP+HDBSCAN of arabinogalactan regions (0=no cluster assigned,1=type a, 2=type b, etc.)
  • nagreg.clust = Cluster based on UMAP+HDBSCAN of non-arabinogalactan non-fasciclin regions (0=no cluster assigned,1=type a, 2=type b, etc.)
  • interP.clust = Cluster based on UMAP+HDBSCAN of inter-proline distance (0=no cluster assigned,1=type a, 2=type b, etc.)
  • genus & species = Taxonomy of the organism containing the sequence
  • tax.name = Broad taxonomic group of organism containing the sequence (not necessarily a monophyletic group)
  • [x].col = colour used in diagrams for sequences in that cluster
  • ngly.site.[x] = Boolean (true/false) of whether the sequence contains an nglycosylation motif at that position in the sequence. Includes a number to indicate domain within a FLA with 2-fasciclin domains (see figs 2 & S8 for positions)

Supp data file 2

Multiple sequence alignments as fasta files for all 2644 fasciclin domains, as well as separately for each cluster A-R.

Naming:

  • Sequence names = sequence name (constructed as: G[fas.clust] X[number] fas [fas.count] of [fas.max] ; see supp data file 1 fields)
  • File names = Cluster based on UMAP+HDBSCAN of fasciclin domain sequence (0=no cluster assigned, 1=type A, 2=type B, etc.)


Supp data file 3

Phylogenies as newick files for all 2644 fasciclin domains, as well as separately for each cluster A-R.

Naming:

  • Sequence names = sequence name (constructed as: G[fas.clust] X[number] fas [fas.count] of [fas.max] ; see supp data file 1 fields)
  • File names = Cluster based on UMAP+HDBSCAN of fasciclin domain sequence (0=no cluster assigned, 1=type A, 2=type B, etc.)

Supp data file 4

An [R] script to perform the analyses shown in the publication. See also github repo TS404/FLAnnotator.



Funding

La Trobe Research Focus Area grant 2000004372

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