DATASET S2: ORFs prediction from the Transcriptomic profile of the cockle Cerastoderma edule exposed to Diarrhetic Shellfish Toxins seasonal contamination

Published: 20 October 2021| Version 2 | DOI: 10.17632/bgps766mxp.2
Contributors:
Dany Domínguez-Pérez,
,

Description

Resulting .fasta and .gff files corresponding to the Open Reading Frames (ORFs) prediction obtained from the de novo transcriptome assembly and clustering analyses in the article: Transcriptomic profile of the cockle Cerastoderma edule exposed to Diarrhetic Shellfish Toxins seasonal contamination. Domínguez-Pérez, D. et al., 2021. Ce_assembly_unique_CDS.fasta: The corresponding nucleotide .fasta file of the Protein Coding Sequences (CDS) obtained by six-frame translation with TransDecoder v5.5.0., considering a minimum length of 100 amino acids for open reading frames (ORFs), homology to known proteins via Pfam searches, and the best/longest isoform per gene. Ce_assembly_unique_proteins.fasta: The resulting amino acid .fasta file of the Protein Coding Sequences (CDS) obtained by six-frame translation with TransDecoder v5.5.0., considering a minimum length of 100 amino acids for open reading frames (ORFs), homology to known proteins via Pfam searches, and the best/longest isoform per gene. Ce_assembly_unique_ORFs.gff: The corresponding .gff file of the Protein Coding Sequences (CDS) obtained by six-frame translation with TransDecoder v5.5.0., considering a minimum length of 100 amino acids for open reading frames (ORFs), homology to known proteins via Pfam searches, and the best/longest isoform per gene. predict_coding_regions_results_assembled_transcripts_clustering.pdf: Summary of the ORFs prediction with TransDecoder v5.5.0., considering a minimum length of 100 amino acids for open reading frames (ORFs), homology to known proteins via Pfam searches, and the best/longest isoform per gene. predict_coding_regions_summary_assembled_transcripts_clustering.pdf: The figure depicts the summary and relative representation of complete, partial and internal ORFs obtained from the de novo transcriptome assembly of C. edule.

Files

Institutions

  • Universidade do Porto Centro Interdisciplinar de Investigacao Marinha e Ambiental
  • Universidade do Porto

Categories

Transcriptomics, Aquatic Toxicology, Coding (DNA)

Licence