Tachiuo

This repository contains the structural, functional and topological annotation of Trichiurus japonicus. For fasta files, the nuclear genome itself is available in NCBI. Here we deposited only mitochondria genome, and structural annotation result. Class File name Tools Database Sequence assembly T_jap_mito.fasta – – Repeat annotation T_jap_repeat.gffT_jap_repeat_table Tetools 1.89.2 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 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 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 –