Supplementary_data_and_material

Supplementary Data and Material

This directory contains Supplementary Data and Material for

Genome-scale detection of positive selection in 9 primates predicts human-virus evolutionary conflicts Robin van der Lee, Laurens Wiel, Teunis J.P. van Dam, Martijn A. Huynen
Nucleic Acids Research 2017; https://doi.org/10.1093/nar/gkx704

Centre for Molecular and Biomolecular Informatics - Radboud Institute for Molecular Life Sciences
Radboud university medical center
Nijmegen, The Netherlands

Correspondence: robinvanderlee AT gmail DOT com

If you found this resource useful, please consider citing the paper.

Original coding and proteins sequences used in our analyses

• Protein-coding DNA sequences
  cds_sequences_11170_genes.tar.gz
  (11,170 files, 9 sequences per file, 1 per primate)

• Protein sequences
  protein_sequences_11170_genes.tar.gz
  (11,170 files, 9 sequences per file, 1 per primate)

PRANK alignments, filtered and masked using GUIDANCE and TCS

• Protein-coding DNA sequence alignments
  prank-codon-guidance-tcs-masked-species-sorted.aln__11096.tar.gz
N: undetermined nucleotides
  n: masked nucleotides

• Translated alignments
  prank-codon-guidance-tcs-masked-species-sorted.aln.translated__11096.tar.gz
X: undetermined amino acids
  o: masked amino acids

• Mapping tables of the alignment column to the position in the human sequence
  prank-codon-guidance-tcs-masked-species-sorted.aln.translated.mapping-table__11096.tar.gz
  Column 1: human amino acid
  Column 2: columns number of the alignment
  Column 3: human sequence position
  

• Concatenation of the 11,096 protein-coding DNA sequence alignments
  concatenated_alignment__11096_genes__9primates__cds.prank-codon-guidance-tcs-masked-species-sorted.aln.fa.gz concatenated_alignment__11096_genes__9primates__cds.prank-codon-guidance-tcs-masked-species-sorted.aln.phy.gz

Visualization and quality control of alignments and positive selection profiles

• Barcode plots of positive selection profiles
  

  • Just the curated set of 331 positively selected genes (PSG): barcode_plots__331_PSG.tar.gz
    
  • All 416 original, apparent positive selected genes (aPSG): barcode_plots__416_aPSG.tar.gz
    

• Jalview alignment annotations
  jalview_alignment_annotations__331_PSG.tar.gz
jalview_alignment_annotations__416_aPSG.tar.gz

• Jalview sequence annotations
  jalview_sequence_annotations__331_PSG.tar.gz
jalview_sequence_annotations__416_aPSG.tar.gz
  

Jalview annotation files contain annotations for the positively selected residues (PSR), as well as exon coordinates mapped to protein sequences. They can be loaded together with the correct corresponding alignment using (on Mac):

Java	-Djava.ext.dirs=/Applications/Jalview/lib/
	-cp /Applications/Jalview/jalview.jar jalview.b.Jalview
	-open <ENSEMBL_ID>__cds.prank-codon-guidance-tcs-masked-species-sorted.aln.translated.fa
	-annotations <ENSEMBL_ID>.jalview_aln_feature
	-features <ENSEMBL_ID>.jalview_seq_feature

Configuration files for PAML codeml

• Inference of reference phylogenetic trees
  codeml_M0_F3X4_tree.ctl
codeml_M0_F61_tree.ctl
  

• Inference of positive selection
  codeml_M1avM2a_F3X4__large-scale-analysis__template.ctl
codeml_M1avM2a_F61__large-scale-analysis__template.ctl
codeml_M7vM8_F3X4__large-scale-analysis__template.ctl
codeml_M7vM8_F61__large-scale-analysis__template.ctl
  

Phylogenetic trees

• codeml reference phylogenetic trees
  codeml_M0_tree__unrooted_tree__F3X4.tre
codeml_M0_tree__unrooted_tree__F61.tre
  

• Other phylogenetic trees
  Ensembl78__9primates__with_taxon_id__unrooted.tre
Perelman_et_al__9primates__unrooted.tre
RAxML_bestTree__9primates__unrooted.tre
  

GUIDANCE source code fix for running PRANK

• guidance_prank_fix.pdf
• Guidance__prank_fix.pm