Add new ncbi translation code (#307)

Add new ncbi translation code
BioJulia · Jun 24, 2024 · af67daf · af67daf
1 parent cbb5397
commit af67daf
Show file tree

Hide file tree

Showing 3 changed files with 14 additions and 0 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,9 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
 ## [UNRELEASED]
+
+* Add new `ncbi_tranlation_table` of the 15th genetic code (i.e `blepharisma_macronuclear_genetic_code`)
+
 * Relax requirement of `decode`, such that it no longer needs to check for
   invalid data. Note that this change is not breaking, since it is not possible
   for correctly-implemented `Alphabet` and `BioSequence` to store invalid data.

diff --git a/docs/src/transforms.md b/docs/src/transforms.md
@@ -167,6 +167,7 @@ Translation Tables:
  12. The Alternative Yeast Nuclear Code (alternative_yeast_nuclear_genetic_code)
  13. The Ascidian Mitochondrial Code (ascidian_mitochondrial_genetic_code)
  14. The Alternative Flatworm Mitochondrial Code (alternative_flatworm_mitochondrial_genetic_code)
+ 15. Blepharisma Macronuclear Code (blepharisma_macronuclear_genetic_code)
  16. Chlorophycean Mitochondrial Code (chlorophycean_mitochondrial_genetic_code)
  21. Trematode Mitochondrial Code (trematode_mitochondrial_genetic_code)
  22. Scenedesmus obliquus Mitochondrial Code (scenedesmus_obliquus_mitochondrial_genetic_code)

diff --git a/src/geneticcode.jl b/src/geneticcode.jl
@@ -252,6 +252,16 @@ Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
 Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
 """
 
+@register_ncbi_gencode 15 blepharisma_macronuclear_genetic_code """
+15. Blepharisma Macronuclear Code
+
+  AAs  = FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
+Starts = ----------*---*--------------------M----------------------------
+Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+"""
+
 @register_ncbi_gencode 16 chlorophycean_mitochondrial_genetic_code """
 16. Chlorophycean Mitochondrial Code