brianjohnhaas
commented
3 years ago hi,
most of trinotate revolves around protein homologies, and most users won't have input sequences that will allow for sufficient homology detection based on blastn. You don't need to perform searches based on transdecoder proteins, though. It does support blastx searches with input transcripts.
On Sat, Dec 19, 2020 at 5:35 AM Stephane Plaisance notifications@github.com wrote:
Could blastn be added as source or is the relational system aminoacid coordinate based and refusing cDNA coordinate information?
It may be useful since my data is from ONT and probably a lot of ORFs are broken by indels and sequencing errors. Additionally, I can not easily error correct the 85000 transcripts I have as it would take ages. I expect that the cDNA to cDNA alignments will span longer distances. Can I fake the import as a blastp or blastx or will this lead to corruption? thanks for your feedback and ideas
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splaisan
Could blastn be added as source or is the relational system aminoacid coordinate based and refusing cDNA coordinate information?
It may be useful since my data is from ONT and probably a lot of ORFs are broken by indels and sequencing errors. Additionally, I can not easily error correct the 85000 transcripts I have as it would take ages. I expect that the cDNA to cDNA alignments will span longer distances. Can I fake the LOAD_custom_blast import as a blastp or blastx or will this lead to corruption? thanks for your feedback and ideas