HajkD / dNdS_database

A collection of genome wise dN/dS calculations generated with orthologr

Genome wide synonymous versus non-synonymous substitution rates dN/dS

A collection of genome wide dN/dS calculations of orthologous genes generated with the comparative genomics tool orthologr

This page hosts a collection of synonymous versus non-synonymous substitution rate dN/dS maps of several pairwise genome comparisons generated with orthologr.

Users may feel free to use this data for their research purposes.

Please cite the orthologr publication when using any of the dN/dS maps for your publication:

Drost et al. 2015. Evidence for Active Maintenance of Phylotranscriptomic Hourglass Patterns in Animal and Plant Embryogenesis. Mol. Biol. Evol. 32 (5): 1221-1231. doi:10.1093/molbev/msv012

E.g. by referring to orthologr:

"Synonymous versus non-synonymous substitution rates between species X and species Y were calculated using the R package orthologr (Drost et al., 2015) using the parameter configuration eval = 1E-5, ortho_detection = "RBH", aa_aln_type = "pairwise", aa_aln_tool = "NW", codon_aln_tool = "pal2nal", and dnds_est.method = "Comeron"."

The computationally reproducible scripts used to generate each dNdS map can be found at /reproducible_scripts/.

Available dNdS maps

Homo sapiens versus Mus musculus

The genome versions and coding sequence versions used to generate the H sapiens vs M musculus dNdS maps can be found at /data_version/.

After downloading the file Hs_vs_Mm_dNdS.csv users can import the dNdS map into R by running:

library(readr)
# import dNdS map
Hs_vs_Mm_dNdS <- readr::read_csv("Hs_vs_Mm_dNdS.csv")
Hs_vs_Mm_dNdS

   query_id                               subject_id                                  dN    dS   dNdS
   <chr>                                  <chr>                                    <dbl> <dbl>  <dbl>
 1 lcl|NC_000001.11_cds_NP_000007.1_4683  lcl|NC_000069.6_cds_NP_031408.1_14466   0.0597 0.829 0.0720
 2 lcl|NC_000001.11_cds_NP_000020.1_10709 lcl|NC_000074.6_cds_NP_031454.3_37923   0.288  0.728 0.395 
 3 lcl|NC_000001.11_cds_NP_000060.2_9320  lcl|NC_000067.6_cds_NP_001074492.1_3195 0.0428 0.457 0.0935
 4 lcl|NC_000001.11_cds_NP_000089.1_4041  lcl|NC_000070.6_cds_NP_034079.2_16642   0.0677 0.449 0.151 
 5 lcl|NC_000001.11_cds_NP_000101.2_5306  lcl|NC_000069.6_cds_NP_740748.1_13710   0.0560 0.530 0.106 
 6 lcl|NC_000001.11_cds_NP_000121.2_8444  lcl|NC_000067.6_cds_NP_032002.1_3789    0.174  0.568 0.306 
 7 lcl|NC_000001.11_cds_NP_000134.2_10958 lcl|NC_000067.6_cds_NP_034339.2_4227    0.0394 0.494 0.0797
 8 lcl|NC_000001.11_cds_NP_000138.2_1730  lcl|NC_000070.6_cds_NP_077205.3_18084   0.0933 0.568 0.164 
 9 lcl|NC_000001.11_cds_NP_000177.2_9184  lcl|NC_000067.6_cds_NP_034018.2_3287    0.268  0.628 0.426 
10 lcl|NC_000001.11_cds_NP_000182.2_1729  lcl|NC_000070.6_cds_NP_032280.2_18085   0.0630 0.545 0.116 
 ... with 25,051 more rows