This is the command TransDecoder.Predict that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
Transdecoder - Transcriptome Protein Prediction
USAGE
Required:
-t <string> transcripts.fasta
Common options:
--retain_long_orfs <int> retain all ORFs found that are equal or longer than these many nucleotides even if no other evidence
marks it as coding (default: 900 bp => 300aa)
--retain_pfam_hits <string> /path/to/pfam_db.hmm to search
using hmmscan (which should be accessible via your PATH setting)
--retain_blastp_hits <string>
Advanced options
--train <string> FASTA file with ORFs to train Markov Mod for protein identification; otherwise
longest non-redundant ORFs used
-T <int> If no --train, top longest ORFs to train Markov Model (hexamer stats) (default: 500)
2015-12-28 TRANSDECODER.PREDICT(1)
Use TransDecoder.Predict online using onworks.net services
