Tachiuo

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. 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 –