TransDecoder reviews and mentions

• What are you using for ORF/gene prediction these days (prokaryotes, viruses, and de novo transcriptomes)?
  1 project | /r/bioinformatics | 8 Feb 2022

  TransDecoder was never officially published in a paper and v5.5.0 came out in 2018.

• Identifying protein coding genes from fna and gff files
  1 project | /r/bioinformatics | 21 Jul 2021
• Is there a way to translate all ORFs on all contigs of a given bioproject on NCBI and write them all out as fasta?
  1 project | /r/bioinformatics | 18 Mar 2021

  I believe Transdecoder (https://github.com/TransDecoder/TransDecoder/wiki) might help you. If you wanted to learn how to do this yourself, it's one of the Rosalind challenges (http://rosalind.info/problems/orf/) that I show how to solve in a new Python/bioinformatics book I'm releasing with O'Reilly. I'd be happy to share the first five chapters if you are curious. DM for details.

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