Mismatching initial residues in Compara protein member sequences |
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| Affects: Ensembl 114 | Fix Version: Ensembl 115 |
| Following improvements to the behaviour of Transcript::translate in the Ensembl core Perl API taking effect in release 114, an initial CTG codon may be translated under the standard genetic code to methionine (M), where previously it would have been translated to a leucine (L).As a result, some protein member sequences — input to comparative analyses before this change in translation behaviour — start with a leucine, while the corresponding translation obtained via the Ensembl core API starts with a methionine.
The resulting sequence mismatches affect 43,991 proteins in Ensembl Vertebrates, 15,747 in Ensembl Plants, 8,879 in Ensembl Metazoa, and 3,258 in Pan-taxonomic Compara. We aim to correct more than 80% of these mismatching sequences in release 115, with the remaining mismatches to be fixed in subsequent releases as comparative datasets are updated. |
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| Workaround: There is currently no workaround. | |
Anopheles gambiae transcript de-sync between CoreDB and Variation DB |
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| Affects: Ensembl 114 | Fix version: Ensembl 115 |
| There is a known issue between the core and variation DB of Anopheles gambiae (production_name -> anopheles_gambiae). The Automation team discovered the issue when running the full suite of DCsThis issue is seemingly due to the submitted update to the core itself and handed over as part of Ensembl 114. Whereby community annotation update to the gene set resulted in some genes being dropped\altered. This change in gene set was not reflected in an appropriate update to the variation DB.
Intentions will be to rerun the transcript variation pipeline and correct this bug for Ensembl 115. |
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| Workaround: No work around, except using most up to date datasets. | |
Large number of ancient paralogies for Triticum aestivum Kariega in a Wheat cultivar supertree |
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| Affects: Ensembl 113, Ensembl 114 | Fix versions: Ensembl 115 |
| During preparation of Wheat cultivar protein trees for Ensembl release 113, it became apparent that supertree PTHR11439_SF127 has approximately 40,000 genes in Triticum aestivum cultivar Kariega. Generation of the 261 million ancient paralogies between these genes took two weeks, and it would not have been possible to include them in Ensembl Plants 113 without delaying the release. | |
| Workaround: A cross-section of the relevant ancient paralogies was loaded during production, involving genes with stable IDs TraesKAR6A01G0279700, TraesKAR7B01G0056390, TraesKAR7B01G0463280 and TraesKAR1D01G0304830. Due to the large number of paralogies involved, these may fail to load correctly on the Ensembl Plants website, though it should be possible to access them via the Ensembl REST API and Compara Perl API.A file containing data on these 40,000 genes is available for download at the following location on the Ensembl Genomes FTP site:http://ftp.ensemblgenomes.org/pub/release-60/plants/emf/ensembl-compara/homologies/Compara.113.protein_wheat_cultivars.other_paralogies.cds.fasta.gz | |
Drop in Cebus imitator ncRNA paralogs from 110 to 111 |
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| Affects: Ensembl 111, Ensembl 112, Ensembl 113, Ensembl 114 | Fix version: Ensembl 115 |
| In Ensembl 111, there was a significant drop (relative to release 110) in the number of ncRNA paralogues for Cebus imitator.This was due to the application in this species of a paralogue filter that was intended for use with low-coverage 2X genomes. | |
| Workaround: Both species are in 110. We recommend that the users interested in ncRNA paralogues for this species to check out the 110 archive. | |
Avena sativa cv. Sang homoeologues misclassified as paralogues |
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| Affects: Ensembl 109, Ensembl 110, Ensembl 111, Ensembl 112, Ensembl 113, Ensembl 114 | Fix version: Ensembl 115 |
| Due to a data synchronisation issue, Avena sativa cultivar Sang was loaded into Plants Compara databases without subgenome component information.As a result, homologues that would otherwise be classified as homoeologues will have been annotated as paralogues. | |
| Workaround: There is currently no workaround. | |