Editing Genetic code (section)

=== Inference ===
Variant genetic codes used by an organism can be inferred by identifying highly conserved genes encoded in that genome, and comparing its codon usage to the amino acids in homologous proteins of other organisms. For example, the program FACIL infers a genetic code by searching which amino acids in homologous protein domains are most often aligned to every codon. The resulting amino acid (or stop codon) probabilities for each codon are displayed in a genetic code logo.<ref name="DutilhJurgelenaite2011">{{cite journal | vauthors = Dutilh BE, Jurgelenaite R, Szklarczyk R, van Hijum SA, Harhangi HR, Schmid M, de Wild B, Françoijs KJ, Stunnenberg HG, Strous M, Jetten MS, Op den Camp HJ, Huynen MA | title = FACIL: Fast and Accurate Genetic Code Inference and Logo | journal = Bioinformatics | volume = 27 | issue = 14 | pages = 1929–33 | date = Jul 2011 | pmid = 21653513 | doi = 10.1093/bioinformatics/btr316 | pmc=3129529}}</ref>

As of January 2022, the most complete survey of genetic codes is done by Shulgina and Eddy, who screened 250,000 prokaryotic genomes using their Codetta tool. This tool uses a similar approach to FACIL with a larger [[Pfam]] database. Despite the NCBI already providing 27 translation tables, the authors were able to find new 5 genetic code variations (corroborated by tRNA mutations) and correct several misattributions.<ref>{{cite journal |last1=Shulgina |first1=Y |last2=Eddy |first2=SR |title=A computational screen for alternative genetic codes in over 250,000 genomes. |journal=eLife |date=9 November 2021 |volume=10 |doi=10.7554/eLife.71402 |pmid=34751130|pmc=8629427 |doi-access=free }}</ref> Codetta was later used to analyze genetic code change in [[ciliates]].<ref>{{cite journal |last1=Chen |first1=W |last2=Geng |first2=Y |last3=Zhang |first3=B |last4=Yan |first4=Y |last5=Zhao |first5=F |last6=Miao |first6=M |title=Stop or Not: Genome-Wide Profiling of Reassigned Stop Codons in Ciliates. |journal=Molecular Biology and Evolution |date=4 April 2023 |volume=40 |issue=4 |doi=10.1093/molbev/msad064 |pmid=36952281 |pmc=10089648}}</ref>