Data associated with the reannotation of repeats in the Octopus vulgaris genome assembly (ASM119413v2)
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2026
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| _version_ | 1866902282571874304 |
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| author | Bonar, Maegwin Elliott, Tyler A. Ahmadi, Mirza A M Cottenie, Karl Linquist, Stefan |
| author_facet | Bonar, Maegwin Elliott, Tyler A. Ahmadi, Mirza A M Cottenie, Karl Linquist, Stefan |
| contents | <p>This is the repeat annotation data generated in "Biological implications of a detailed repeat annotation in Octopus vulgaris" (https://doi.org/10.64898/2026.03.03.709284) for the Octopus vulgaris ASM119413v2 assembly (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_001194135.2/). This includes:</p> <p>-the GFF file of the repeat annotation (OctVulg_genome_annotation_only.filteredRepeats.gff)</p> <p>-this is the raw annotation before TE sequences smaller than 100 bp were filtered out for calculating summary information </p> <p>-the FASTA file of reference TE sequences used as well as the new, curated TE and other repeat consensus sequences that were generated (O_vulgaris_and_reference_repeats_Oct24-2.fasta)</p> <p>-sequence headers for reference sequences start with 'REFERENCE', and with 'Ovulg' for new consensus sequences. This includes several consensus sequences of Zinc-finger gene arrays that were noticed during curation (#ZF-array) as well as satellites, unknown repeats and some RNA loci. Characters before the '#' symbol are strings which are unique to each sequence</p> <p>The R markdown file (GBE_O_vulgaris_repeat_annotation.Rmd) contains the code for filtering the GFF file for short TE hits, for young elements and for recreating Figures 1 and 2, including the hotspot/coldspot analysis. Input required for this pipeline is the GFF file of the repeat annotation (OctVulg_genome_annotation_only.filteredRepeats.gff) and the Octopus vulgaris ASM119413v2 assembly (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_001194135.2/)</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_20056424 |
| institution | Zenodo |
| language | eng |
| publishDate | 2026 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Data associated with the reannotation of repeats in the Octopus vulgaris genome assembly (ASM119413v2) Bonar, Maegwin Elliott, Tyler A. Ahmadi, Mirza A M Cottenie, Karl Linquist, Stefan DNA Transposable Elements Repetitive Sequences, Nucleic Acid Mollusca Cephalopoda <p>This is the repeat annotation data generated in "Biological implications of a detailed repeat annotation in Octopus vulgaris" (https://doi.org/10.64898/2026.03.03.709284) for the Octopus vulgaris ASM119413v2 assembly (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_001194135.2/). This includes:</p> <p>-the GFF file of the repeat annotation (OctVulg_genome_annotation_only.filteredRepeats.gff)</p> <p>-this is the raw annotation before TE sequences smaller than 100 bp were filtered out for calculating summary information </p> <p>-the FASTA file of reference TE sequences used as well as the new, curated TE and other repeat consensus sequences that were generated (O_vulgaris_and_reference_repeats_Oct24-2.fasta)</p> <p>-sequence headers for reference sequences start with 'REFERENCE', and with 'Ovulg' for new consensus sequences. This includes several consensus sequences of Zinc-finger gene arrays that were noticed during curation (#ZF-array) as well as satellites, unknown repeats and some RNA loci. Characters before the '#' symbol are strings which are unique to each sequence</p> <p>The R markdown file (GBE_O_vulgaris_repeat_annotation.Rmd) contains the code for filtering the GFF file for short TE hits, for young elements and for recreating Figures 1 and 2, including the hotspot/coldspot analysis. Input required for this pipeline is the GFF file of the repeat annotation (OctVulg_genome_annotation_only.filteredRepeats.gff) and the Octopus vulgaris ASM119413v2 assembly (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_001194135.2/)</p> |
| title | Data associated with the reannotation of repeats in the Octopus vulgaris genome assembly (ASM119413v2) |
| topic | DNA Transposable Elements Repetitive Sequences, Nucleic Acid Mollusca Cephalopoda |
| url | https://doi.org/10.5281/zenodo.20056424 |