TransDecoder (Find Coding Regions Within Transcripts)
TransDecoder identifies candidate coding regions within transcript sequences,
such as those generated by de novo RNA-Seq transcript assembly using Trinity,
or constructed based on RNA-Seq alignments to the genome using Tophat and
Cufflinks.
TransDecoder identifies likely coding sequences based on the following
criteria:
-
a minimum length open reading frame (ORF) is found in a transcript sequence
-
a log-likelihood score similar to what is computed by the
GeneID software is > 0.
-
the above coding score is greatest when the ORF is scored in the 1st reading
frame as compared to scores in the other 2 forward reading frames.
-
if a candidate ORF is found fully encapsulated by the coordinates of another
candidate ORF, the longer one is reported. However, a single transcript can
report multiple ORFs (allowing for operons, chimeras, etc).
-
a PSSM is built/trained/used to refine the start codon prediction.
-
optional the putative peptide has a match to a Pfam domain above the
noise cutoff score.
Location:
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$ which TransDecoder.LongOrfs
/local/cluster/bin/TransDecoder.LongOrfs
$ TransDecoder.LongOrfs --version
TransDecoder.LongOrfs 5.5.0
$ which TransDecoder.Predict
/local/cluster/bin/TransDecoder.Predict
$ TransDecoder.Predict --version
TransDecoder.Predict 5.5.0
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Util dir:
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$ ls /local/cluster/TransDecoder/util/
bin/ gff3_file_to_proteins.pl* refine_gff3_group_iso_strip_utrs.pl*
cdna_alignment_orf_to_genome_orf.pl* gff3_gene_to_gtf_format.pl* refine_hexamer_scores.pl*
compute_base_probs.pl* gtf_genome_to_cdna_fasta.pl* remove_eclipsed_ORFs.pl*
exclude_similar_proteins.pl* gtf_to_alignment_gff3.pl* score_CDS_likelihood_all_6_frames.pl*
fasta_prot_checker.pl* gtf_to_bed.pl* select_best_ORFs_per_transcript.pl*
ffindex_resume.pl* misc/ seq_n_baseprobs_to_loglikelihood_vals.pl*
gene_list_to_gff.pl* nr_ORFs_gff3.pl* start_codon_refinement.pl*
get_FL_accs.pl* pfam_mpi.pbs* train_start_PWM.pl*
get_longest_ORF_per_transcript.pl* pfam_runner.pl* uri_unescape.pl*
get_top_longest_fasta_entries.pl* PWM/
gff3_file_to_bed.pl* __pwm_tests/
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help message:
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$ TransDecoder.Predict -h
########################################################################################
# ______ ___ __
# /_ __/______ ____ ___ / _ \___ _______ ___/ /__ ____
# / / / __/ _ `/ _\(_-</ // / -_) __/ _ \/ _ / -_) __/
# /_/ /_/ \_,_/_//_/___/____/\__/\__/\___/\_,_/\__/_/ .Predict
#
########################################################################################
#
# Transdecoder.LongOrfs|http://transdecoder.github.io> - Transcriptome Protein Prediction
#
#
# Required:
#
# -t <string> transcripts.fasta
#
# Common options:
#
#
# --retain_long_orfs_mode <string> 'dynamic' or 'strict' (default: dynamic)
# In dynamic mode, sets range according to 1%FDR in random sequence of sameGC content.
#
#
# --retain_long_orfs_length <int> under 'strict' mode, retain all ORFs found that are equal or longer than these many nucleotides even if no other evidence
# marks it as coding (default: 1000000) so essentially turned off by default.)
#
# --retain_pfam_hits <string> domain table output file from running hmmscan to search Pfam (see transdecoder.github.io for info)
# Any ORF with a pfam domain hit will be retained in the final output.
#
# --retain_blastp_hits <string> blastp output in '-outfmt 6' format.
# Any ORF with a blast match will be retained in the final output.
#
# --single_best_only Retain only the single best orf per transcript (prioritized by homologythen orf length)
#
# --output_dir | -O <string> output directory from the TransDecoder.LongOrfs step (default: basename( -t val ) + ".transdecoder_dir")
#
# -G <string> genetic code (default: universal; see PerlDoc; options: Euplotes, Tetrahymena, Candida, Acetabularia, ...)
#
# --no_refine_starts start refinement identifies potential start codons for 5' partial ORFs using a PWM, process on by default.
#
## Advanced options
#
# -T <int> Top longest ORFs to train Markov Model (hexamer stats) (default: 500)
# Note, 10x this value are first selected for removing redundancies,
# and then this -T value of longest ORFs are selected from the non-redundant set.
# Genetic Codes
#
#
# --genetic_code <string> Universal (default)
#
# Genetic Codes (derived from: https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi)
#
#
Acetabularia
Candida
Ciliate
Dasycladacean
Euplotid
Hexamita
Mesodinium
Mitochondrial-Ascidian
Mitochondrial-Chlorophycean
Mitochondrial-Echinoderm
Mitochondrial-Flatworm
Mitochondrial-Invertebrates
Mitochondrial-Protozoan
Mitochondrial-Pterobranchia
Mitochondrial-Scenedesmus_obliquus
Mitochondrial-Thraustochytrium
Mitochondrial-Trematode
Mitochondrial-Vertebrates
Mitochondrial-Yeast
Pachysolen_tannophilus
Peritrich
SR1_Gracilibacteria
Tetrahymena
Universal
#
# --version show version (5.5.0)
#
#########################################################################################
$ TransDecoder.LongOrfs
########################################################################################
# ______ ___ __
# /_ __/______ ____ ___ / _ \___ _______ ___/ /__ ____
# / / / __/ _ `/ _\(_-</ // / -_) __/ _ \/ _ / -_) __/
# /_/ /_/ \_,_/_//_/___/____/\__/\__/\___/\_,_/\__/_/ .LongOrfs
#
########################################################################################
#
# Transdecoder.LongOrfs|http://transdecoder.github.io> - Transcriptome Protein Prediction
#
#
# Required:
#
# -t <string> transcripts.fasta
#
# Optional:
#
# --gene_trans_map <string> gene-to-transcript identifier mapping file (tab-delimited, gene_id<tab>trans_id<return> )
#
# -m <int> minimum protein length (default: 100)
#
# -G <string> genetic code (default: universal; see PerlDoc; options: Euplotes, Tetrahymena, Candida, Acetabularia)
#
# -S strand-specific (only analyzes top strand)
#
# --output_dir | -O <string> path to intended output directory (default: basename( -t val ) + ".transdecoder_dir")
#
# --genetic_code <string> Universal (default)
#
# Genetic Codes (derived from: https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi)
#
Acetabularia
Candida
Ciliate
Dasycladacean
Euplotid
Hexamita
Mesodinium
Mitochondrial-Ascidian
Mitochondrial-Chlorophycean
Mitochondrial-Echinoderm
Mitochondrial-Flatworm
Mitochondrial-Invertebrates
Mitochondrial-Protozoan
Mitochondrial-Pterobranchia
Mitochondrial-Scenedesmus_obliquus
Mitochondrial-Thraustochytrium
Mitochondrial-Trematode
Mitochondrial-Vertebrates
Mitochondrial-Yeast
Pachysolen_tannophilus
Peritrich
SR1_Gracilibacteria
Tetrahymena
Universal
#
#
# --version show version tag (5.5.0)
#
#########################################################################################
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software ref: https://github.com/TransDecoder/TransDecoder/wiki
research ref: <>