Repository for Data in "Membrane environment imposes unique selection pressures on transmembrane domains of G-protein coupled receptors"

Contents of repository

Of primary interest are alignments and trees:

• guidance_aln_nuc/ and guidance_aln_prot/ contain respectively codon and amino-acid alignments (they correspond), with sites filtered based on Guidance algorithm

• unaligned_sequences/ contain raw sequences (unaligned fasta files) for each ortholog

• trees/ contains all RAxML-inferred trees. All files "*bl_bs.tre" contain bootstrap and branch lengths, whereas other files are just topology

• structures/ contains transmembrane predictions for GPCRHMM

• partitioned_alignments/ contains same data as in guidance_aln_nuc/ except partitioned into extramembrane and transmembrane, based on predictions found in structures/. Files named as:

  • *_extra.fasta are extramembrane (intra and extracellular) domains
  • *_inner.fasta are intracellular domains
  • *_outer.fasta are extracellular domains
  • *_trans.fasta are transmembrane domains
  • *_genome.fasta are full sequences (ie unpartitioned)

Other contents:

• InitialGeneSet/ contains Ensembl and GO annotations for original data collection. Note, many of these sequences end up not being used because they were not GPCRs.
• dssp_files/ contains structural information predicted with DSSP for known GPCR structures in this study
• hyphy/ contains results summaries for models tested, including AIC for no partitioning (null_results.txt), AIC for 2 vs 3 partition schemes (2vs3_partitions_results.txt) and mean evo rates using best model (rel_results.txt)