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.
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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)
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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
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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
- Just the curated set of 331 positively selected genes (PSG):
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Jalview alignment annotations
jalview_alignment_annotations__331_PSG.tar.gz
jalview_alignment_annotations__416_aPSG.tar.gz
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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
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Inference of reference phylogenetic trees
codeml_M0_F3X4_tree.ctl
codeml_M0_F61_tree.ctl
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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
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codeml reference phylogenetic trees
codeml_M0_tree__unrooted_tree__F3X4.tre
codeml_M0_tree__unrooted_tree__F61.tre
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Other phylogenetic trees
Ensembl78__9primates__with_taxon_id__unrooted.tre
Perelman_et_al__9primates__unrooted.tre
RAxML_bestTree__9primates__unrooted.tre
guidance_prank_fix.pdf
Guidance__prank_fix.pm