Question on translation engine used - Githubissues

alekseyzimin / EviAnn_release

This is the standalone version of the EviAnn pipeline

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Question on translation engine used #2

Open asan-emirsaleh opened 9 months ago

asan-emirsaleh commented 9 months ago

Hello! Great project. It appeared to be interesting for me to ask your opinion on current ORF reconstruction tools. You have chosen the Transdecoder. Are there shortcomings that are expected to appear? What do you think about Evidential Gene tr2aacds.pl? http://arthropods.eugenes.org/EvidentialGene/evigene/docs/evigene_vs_transdecoder_arabidopsis.txt http://arthropods.eugenes.org/EvidentialGene/evigene/docs/transrate_err_arabid17.txt http://arthropods.eugenes.org/EvidentialGene/evigene/docs/tr2aacds_aaconsensus_item.txt https://www.biorxiv.org/content/10.1101/829184v1.full

May it be possible for EviAnn to add alternative ORF predicting options?

Best regards Asan

alekseyzimin commented 9 months ago

Thank you for your suggestion. Incorporating different ORF finders is something that I may do in the future. Transdecoder is used in a very limited fashion, and it currently works well for its purpose. Transdecoder is only used for finding ORFs in transcripts without corresponding protein alignments and in transcripts where the CDS is messed up. These are in a vast minority.