TABLE 2.
CDS databases used in NMDtxDB
| Database name | Name of NMDtxDB source | Description | Ref. |
|---|---|---|---|
| Ensembl | canonical, ensembl | Uses a comprehensive process to annotate CDSs. The process has both manual and automated steps. It is the preferred choice for transcriptome annotation. | (Yates et al. 2020) |
| Encode Ribo-seq ORFs | riboseq | Identifies and catalogs noncanonical, unannotated translated open reading frames in seven Ribo-seq data sets. | (Mudge et al. 2022) |
| OpenProt | openprot | Identifies known proteins, novel isoforms, and alternative proteins from publicly available proteomics data sets, and backs up its predictions with conservation, translation, and expression evidence. | (Brunet et al. 2021) |
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Data from three databases end into four CDS sources in NMDtxDB. We use the Ensembl database for two sources: canonical and ensembl. For annotated transcripts, the first uses CDS as is, whereas the second uses the annotated CDS as a template to find the longest CDS for nonannotated transcripts. This process is detailed in the Materials and Methods section (see “Coding sequence curation”).
