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"
, anddnds_est.method = "Comeron"
."
The computationally reproducible scripts used to generate each dNdS map
can be found at /reproducible_scripts/.
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