Meekes, Lisa · Tabaro, Francesco · Bexkens, Michiel · et al.

41 files · 8.2 GB · csv, fasta, pdfdeclared

This record contains the Python software for PEPTiGEN, a tool for generating tryptic peptides from prokaryotic gene sequences and their variants, and the associated antimicrobial resistance (AMR) peptide database. The database is provided as an SQL file and a CSV file containing all genes and predicted peptides. The README file contains explanation of the PEPTiGEN tool. The SQL database schema files contains both the database schema of the SQL database used in the PEPTiGEN analysis as the database schema of the AMR peptide datbase.

Fairlie Reese

9 files · 16 GB · gff, tsvdeclared

master_table_pcg_lnc.tsv: Metadata / information about each transcript isoform (filtered for protein coding and lncRNAs only) merged.gtf: GTF of transcript isoforms transcript_tpm_summary.tsv: TPMs of each transcript isoform PFAM-Filtered-Merged.txt: PFAM domains called in each predicted ORF sequence from each transcript. Filtered for quality and confidence. fetal_dhs_info.tsv - genomic locations of all DHSs, distance from nearest TSS, gene associated with nearest TSS fetal_matrix_binary.tsv - binary matrix with samples (rows) x DHSs (columns) with 1 indicating the presence of a peak in that DHS in that sample at an FDR of 1% fetal_matrix_density.tsv - matrix of read depth normalized counts fetal_matrix_vst.tsv - matrix of vst normalized counts (like deseq) fetal_meta.tsv - metadata of fetal samples, should include the ln_number for DNase, which wil match the rows of the matricies, and the per sample matching ln_number and other identifiers for short read and long read RNA seq, as indicated by the column titles

Formaggioni, Alessandro

6 files · 3.4 GB · fasta, gff, zipdeclared

Genome assembly of Cardita leana (Bivalvia: Archiheterodonta) and the associated gene models predicted with AUGUSTUS. The 'Tree' folder contains species trees inferred using different tree reconstruction programs. The MCMC_analysis folder contains inputs and ouputs for every MCMCTree analysis

Pastor Durántez, Eduardo · Diez Casero, Julio Javier

2 files · 15 MB · gffdeclared

Curated, high-confidence structural gene annotation of Phytophthora plurivora (strain TJ71), provided in GFF3 format (15,415 gene models; gene, mRNA, exon, and CDS features). The annotation was generated with a BRAKER3-based structural prediction pipeline, followed by a custom curation workflow combining transcript deduplication, repeat- and expression-aware filtering, a heuristic homology-and-topology scoring scheme, and directed manual curation. This dataset was produced as part of the associated manuscript describing the genome annotation and two-speed genome architecture of P. plurivora . This annotation is built on the previously published genome assembly available at NCBI GenBank under accession ASM3002794v1. The genome FASTA itself is not included in this deposit. See the accompanying README.txt for full file description, methods summary, and locus tag conventions.