Convert Protein Codon to Genome Coordinates

I needed a way to check if a few codons from different proteins were covered in a next-generation sequencing panel. This sounds relatively easy to do, but proves to be a bit difficult. Here are steps to do this.

(1) Use Biomart ID converter to find the Ensembl protein ID for your protein of interest.
(2) Use Ensembl GET map/translation/:id/:region to find the genomic coordinates of the codon of interest using the following script:


ENSP00000288602 is the Ensembl protein ID for your protein of interest (example: BRAF gene)
100..100 are the start and stop codons (example: just codon 100)

The result is a JSON formatted string like this:
{"mappings":[{"assembly_name":"GRCh38","end":140834815,"seq_region_name":"7","gap":0,"strand":-1,"coord_system":"chromosome","rank":0,"start":140834813}]}

This indicates that codon 100 of the BRAF gene (for this protein transcript) is located at chr7:140834813-140834815. Ensembl uses GRCh38. If you need other builds of the genome, use liftOver for converting.

I am sure there are probably more automated ways out there to do this, but this worked for the small subset of codons I needed to check in the design panel. If you have a better way to do this, please share in the comments section.

Generate Random Genomic Positions

Generating random genomic positions or coordinates can be useful in comparing characteristics of a set of genomic loci to that what would be expected from permutations of the underlying genomic distribution.  Below is a Python script to aid in selecting random genomic positions.  The script chooses a chromosome based on probabilities assigned by chromosome length and then chooses a chromosomal position from a uniform distribution of the chromosome's length.  An added gap checking statement is included to ensure the chosen position lies within the accessible genome.  You can choose the number of positions you want, the number of permutations to conduct, the size of the genomic positions, and the genomic build of interest.  A UNIX shell script is included as a wrapper to automatically download needed chromosomal gap and cytoband files as well as run the Python script.  Useage for the UNIX script can be seen by typing ./make_random.sh from the command line after giving the script executable privileges.  An example command would be ./make_random 100 10 1000 hg19.  This command would make 10 .bed files each with 100 random 1Kb genomic regions from the hg19 genome build.  Below are the make_random.sh and make_random.py scripts.