Tachiuo
Year: 2025
Type: article
Abstract: This repository contains the structural, functional and topological annotation of Trichiurus japonicus. For fasta files, the nuclear genome itself is available on NCBI (GCA_050140585.1). Here we deposited only fasta files from mitochondria genome and structural annotation. This updated version includes all predictions outside the 24 chromosomes and mitogenome, whereas v1 contained results from only the 24 chromosomes. Notice: The repeat annotation database used for these deposited results did not include RepBase, despite its mention in the associated publication. The repeat annotation was generated using a custom database based on RepeatModeler and Dfam/FamDB. Class File name Tools Database Sequence assembly T_jap_mito.fasta – – Repeat annotation T_jap_repeat.gffT_jap_repeat_table Tetools 1.89.2 Actinopterygii ortholog sets from partition 0, 2 and 6 of Dfam 3.8Repbase (2018/10/26) Structural annotation T_jap_merged_fix.gff.gz T_jap_merged_fix.gtf.gz braker3:v3.0.7.6mitos (v2.1.9)INFERNAL 1.1.5 (cmscan)tRNAscan‑SE 2.0.12 EukHighConfidenceFilter v1.0 custom python script for merging gff from braker/mitos/infernal/trnascan-se AGAT (v1.4.1) gff to gtf Odbv12/UniProtKB_7898/ncbi_1489894RefSeq 89 MetazoaRfam 15.0 T_jap_combined_gene.faT_jap_combined_trans.faT_jap_combined_CDS.faT_jap_combined_pep.fa parse with custom script, using bedtools (v2.31.1) to soft mask intron and extract sequence extract CDS with gffread (v0.12.7) combined braker3:v3.0.7.6 and mitos (v2.1.9) result and modify .t -> .p and removed * (stop codon) - Functional annotation T_jap_diamond.tsv diamond (v2.1.10.164) nr.000–125 T_jap_interproscan_result.tsv InterProScan‑5.73‑104.0 AntiFam-8.0CDD-3.21Coils-2.2.1FunFam-4.3.0Gene3D-4.3.0Hamap-2023_05MobiDBLite-4.0NCBIfam-17.0PANTHER-19.0Pfam-37.2PIRSF-3.10PIRSR-2023_05PRINTS-42.0ProSitePatterns-2023_05ProSiteProfiles-2023_05SFLD-4SMART-9.0SUPERFAMILY-1.75 T_jap_kaas_ghostz.tar.gz KEGG Automatic Annotation Server 2.1ghostz + BBH method Fishes Topological annotation T_jap_deeptmhmm.tsv DeepTMHMM 1.0.24 –
Authors: Lab of Systems and Network Biology, Hsu, Po-Cheng, Chuang, Wei-Hsuan, Hsieh, Ping-Heng, Chen, Shu-Hwa, Chao-lun Allen, Chao-lun Allen, Lin, Chung-Yen
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W6930767860