DOI: 10.5281/zenodo.17828121
title: SupplementaryDataD1 for: Overcoming the widespread flaws in the annotation of vertebrate selenoprotein genes in public databases

description: Supplementary Data D1. Selenoprotein predictions by Selenoprofiles. Here's the content of the included README file for a description of the files included.

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## Directory Overview

### NCBI.selenoprotein_predictions.zip

Contains selenoprotein prediction data sourced from the NCBI database. Inside this file you will find a directory for each species with the following format: {species_name}.{accession_id}

Inside each directory you will find:

- `{species_name}.{accession_id}.sec.011225.gtf` & `{species_name}.{accession_id}.CDS.011225.gtf`  GTF file describing genomic intervals of predicted selenoproteins. The relevant information by Selenoprofiles Orthology and Lineage, as well as the misannotation status, is also available in each row.  **sec gtf file** contains only selenocysteine prediction residues from each selenoprotein gene  **CDS gtf file** contains coding sequence entries for all Selenoprofiles predictions. All those that are not selenoprotein predictions (i.e. Selenoprofiles label is not "selenocysteine") are marked as such.

- `{species_name}.{accession_id}.AGGREGATE.011225.tsv` & `{species_name}.{accession_id}.COMPLETE.011225.tsv`    TSV file describing the (mis)annotation status of predicted selenoprotein genes. Selenoprofiles Orthology and Lineage information is also included.  **COMPLETE tsv file** contains (mis)annotation labels at the transcript level. When multiple annotated transcripts overlap a Selenoprofiles selenoprotein prediction, one label is provided for each.  **AGGREGATE tsv file** contains a single (mis)annotation label per selenoprotein prediction (gene level annotation).

- `output folder`  Folder containing selenoprofiles predictions in two different text formats: **p2g** and **ali** (Selenoprofiles formats, see below and online documentation).   

- `results.sqlite`  SQlite database where selenoprofiles results are saved (Selenoprofiles format, see online documentation).

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### Ensembl.selenoprotein_predictions.zip

Contains selenoprotein prediction data sourced from the Ensembl database. Inside this file you will find a directory for each species with the following format: {species_name}

Inside each directory you will find:

- `{species_name}.sec.011225.gtf` & `{species_name}.CDS.011225.gtf`  GTF file describing genomic intervals of predicted selenoproteins. The relevant information by Selenoprofiles Orthology and Lineage, as well as the misannotation status, is also available in each row.  **sec gtf file** contains only selenocysteine prediction residues from each selenoprotein gene  **CDS gtf file** contains coding sequence entries for all Selenoprofiles predictions. All those that are not selenoprotein predictions (i.e. Selenoprofiles label is not "selenocysteine") are marked as such.

- `{species_name}.AGGREGATE.011225.tsv` & `{species_name}.COMPLETE.011225.tsv`    TSV file describing the (mis)annotation status of predicted selenoprotein genes. Selenoprofiles Orthology and Lineage information is also included.  **COMPLETE tsv file** contains (mis)annotation labels at the transcript level. When multiple annotated transcripts overlap a Selenoprofiles selenoprotein prediction, one label is provided for each.  **AGGREGATE tsv file** contains a single (mis)annotation label per selenoprotein prediction (gene level annotation).

- `output folder`  Folder containing selenoprofiles predictions in two different text formats: **p2g** and **ali** (Selenoprofiles formats, see below and online documentation).

- `results.sqlite`  SQlite database where selenoprofiles results are saved (Selenoprofiles format, see online documentation).

Besides the species listed in the paper, we also provide files for these non-vertebrate species: *Drosophila melanogaster*, *Ciona intestinalis*, *Ciona Savignyi*, *Caenorhabditis elegans* and *Saccharomyces cerevisiae*

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## File Descriptions

### FASTA Files (`*.ali`)

These files contain the selenoprotein family profile sequences, aligned with the Selenoprofiles predicted selenoprotein sequences.**Header format:**  (for Selenoprofiles predictions, not profile sequences) 

Identifier (first word of each title): profile_name.index.label

- `profile_name`: identifies the source profile for the prediction  - `index`: an arbitrary numeric ID  - `label`: identifies the class of predicted gene  (e.g. selenocysteine, cysteine)

Rest of fasta title: - `chromosome`: the contig or chromosome identifier of the prediction- `strand`: the strand (+ or -) of the prediction- `positions`: string of coding exons positions (e.g. 61511-61713,60260-60472), mirroring the information in the GTF file- `species`: quoted species name- `prediction_program`: the predictor program that produced this gene structure (genewise, exonerate or blast)- `target`: the filename of the genome in fasta format---

### GTF Files (`*.gtf`)

These files contain the genomic intervals of selenoprotein predictions.  The `gene_id` column follows the notation:  

profile_name.index.label  (see above for explanation)

Other data has been added:- `filter_status`: Wether selenoprofiles lineage has discarded the prediction or not. - `Annotation`: Annotation status of that selenoprofiles prediction.- `Orthology`: Subfamily classification by selenoprofiles orthology.- `Transcript_id_ens`: ID of annotations (NCBI or Ensembl) overlapping with this selenoprotein prediction.

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### TSV Files (`*.tsv`)

Tab-separated files saving selenoprotein IDs along with their Orthology label and Filtering status after the orthology and lineage utilities by selenoprofiles.

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## Notes

- The datasets are organized separately for NCBI and Ensembl to maintain clarity on source origin.  - The filtering status in TSV files helps in downstream analyses to select high-confidence selenoprotein predictions.  

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*For questions or clarifications, contact us at the email provided in the published manuscript*