Hello, I would need to get the ORFs sequences both nucleotides and translated (aa) from blastx hits. I know transDecoder generate .cds and .pep files corresponding to nucleotide and aminoacids fasta files, but for some transcripts the ORFs found by TransDecoder are not correct whereas blastx correctly identified the ORFs. Thus, I would rather use the ORFs found by blastx than TransDecoder. However, I cannot find a way to get the ORFs sequences, both nucleotide and amino acids, from the blastx results! Is there a way to do that? Thank you! Giulia
I don't think there is a way to obtain translations from BlastX. Blastx translates a nucleotide query sequence in the six possible frames and compares them to protein sequences. The query sequence can be a fragment of a genome, a gene (with introns) or a CDS. Hence, Blastx does not know how to translate your sequences, it can only tell you which virtual translations give significant hits with proteins.
What kind of sequences are you searching for? If you are searching CDS (no introns) you can identify the correct frame in BlastX output and search for the initiating Met. ORFinder (https://www.ncbi.nlm.nih.gov/orffinder/) can be of help here.
Another thing you can do is to download the Blastx output and write a script to extract the translations that hit a protein sequence.
Hope this helps, Federico