2026-10-14T13:08:21Z https://api.figshare.com/v2/oai

oai:figshare.com:article/31860841 2026-10-08T12:55:41Z category_24205 category_24310 item_type_3 month_year_10_2026

<i>Scincus </i><i>mitranus </i>structural and functional annotation Olga Mashkova (22501031) Marwa Abdelhakim (6040190) Fernando Zhapa-Camacho (23627409) Rund Tawfiq (23627423) Kexin Niu (23627428) Maxat Kulmanov (23627438) Mohammed Alarawi (10950982) Magnus Rueping (23627447) Robert Hoehndorf (19654085) Translational and applied bioinformatics Genomics Genome structural annotation Genome functional annotation BRAKER3 KEGG enrichment pathway analysis KofamScan InterProScan search results gene ontogeny (GO) analysis eggNOG-mapper Mitochondrial genome annotation RepeatMasker annotation tables RepeatModeler2 <p dir="ltr">Genome annotation of the chromosome-level diploid assembly of the Eastern sandfish (<i>Scincus mitranus</i>, isolate OM-2025; assembly: figshare DOI 10.6084/m9.figshare.33028703). All files use the assembly's final sequence names; gene and repeat annotation cover the 32 chromosomes.</p><p dir="ltr"><b>Gene models.</b> BRAKER3 (v3.0.8) predicted 31,136 genes (39,948 transcripts) on the soft-masked chromosomes, using OrthoDB protein and Iso-Seq transcript evidence. The final gene set consists of the transcripts whose best SwissProt hit (DIAMOND) has at least 60% identity: 20,821 genes and 27,330 transcripts (10,361 and 10,460 genes in pseudohaplotypes 1 and 2). It is provided as GFF3 with protein and coding sequences, the GenBank product names and locus tags (prefixes ACVTY0 and ACVTY1), and a per-transcript evidence table covering all BRAKER3 models. The complete BRAKER3 annotation is also included.</p><p dir="ltr"><b>Functional annotation.</b> InterProScan 5.61-93.0, PfamScan (Pfam-A 37.4) and KofamScan 1.3.0 (KOfam 2025-08-01) on all BRAKER3 proteins; eggNOG-mapper 2.1.12 (eggNOG 5.0) and KEGG Mapper pathway and module reconstruction on the final gene set.</p><p dir="ltr"><b>Repeat annotation.</b> A species-specific library of 2,361 repeat families built with RepeatModeler2 (v2.0.5); RepeatMasker (v4.1.8) annotation of the chromosomes with this library (43.2% masked; one GFF3 per pseudohaplotype, with the RepeatMasker summary table); and the soft-mask used for gene prediction, the union of RepeatMasker runs with the custom, Dfam and Repbase libraries (44.5% of the chromosomes), as a BED file.</p><p dir="ltr"><b>Mitochondrial genome.</b> Feature table of the mitochondrial genome, GenBank PZ445130.1.</p><p dir="ltr">The README describes every file, and md5sums.txt gives checksums. This deposit accompanies the Scientific Data Data Descriptor of the <i>Scincus mitranus</i> genome assembly.</p> 2026-03-26T13:14:05Z Dataset Dataset 10.6084/m9.figshare.31860841.v3 https://figshare.com/articles/dataset/_i_Scincus_i_i_i_i_mitranus_i_structural_and_functional_annotation/31860841 CC BY 4.0