From b41de1b44b12d5920afea3738232cdcbb9519032 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Camilo=20Garc=C3=ADa?= Date: Thu, 20 Jun 2024 08:45:35 -0500 Subject: [PATCH 1/3] Add new ncbi translation code --- src/geneticcode.jl | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/src/geneticcode.jl b/src/geneticcode.jl index e98df9ef..444db4b1 100644 --- 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 From 9dbb17ea1153c2e273085280d6c35b9bf21a01ec Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Camilo=20Garc=C3=ADa?= Date: Thu, 20 Jun 2024 08:47:27 -0500 Subject: [PATCH 2/3] Update translation docs --- docs/src/transforms.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/src/transforms.md b/docs/src/transforms.md index fdc9e598..efe82145 100644 --- 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) From d4e3173dfe84b27807a2afba2675df30e97e95e0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Camilo=20Garc=C3=ADa?= Date: Thu, 20 Jun 2024 08:55:39 -0500 Subject: [PATCH 3/3] Update CHANGELOG --- CHANGELOG.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index dc3426c5..1af37013 100644 --- 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.