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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.
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
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