TransDecoder¶

TransDecoder identifies candidate coding regions within transcript sequences. The bundle packages version 5.7.1.

Usage example¶

The following command can be executed in the terminal to load the bundle:

1	`module load transdecoder`

The TransDecoder utilities can be run as shown below:

cdna_alignment_orf_to_genome_orf.pl
compute_base_probs.pl
exclude_similar_proteins.pl
fasta_prot_checker.pl
ffindex_resume.pl
gene_list_to_gff.pl
get_FL_accs.pl
get_longest_ORF_per_transcript.pl
get_top_longest_fasta_entries.pl
gff3_file_to_bed.pl
gff3_file_to_proteins.pl
gff3_gene_to_gtf_format.pl
gtf_genome_to_cdna_fasta.pl
gtf_to_alignment_gff3.pl
gtf_to_bed.pl
nr_ORFs_gff3.pl
refine_gff3_group_iso_strip_utrs.pl
refine_hexamer_scores.pl
remove_eclipsed_ORFs.pl
score_CDS_likelihood_all_6_frames.pl
select_best_ORFs_per_transcript.pl
seq_n_baseprobs_to_loglikelihood_vals.pl
start_codon_refinement.pl
TransDecoder.LongOrfs
TransDecoder.Predict

The transdecoder_shell command can be run for a shell in the bundle.

1	`transdecoder_shell`

Performance notes¶

No performance notes available

Recommended resources per session¶

No recommended resources available

Benchmarks¶

No benchmarks available.

Community guides and tutorials¶

No community guides available.

Official site and documentation¶

Licensing information¶

TransDecoder is provided as is.

Primary citation¶

External guides and resources¶

If you know of a guide/tutorial that you have found useful, please help us share it by contacting the HPC staff at hpc@ufs.ac.za