Hy everybody !
I would like to know the proteins encoded by these transcripts and if these proteins are secreted. Here are the steps that I will do to my analysis :
1 / Filter my transcriptome file with blastx against the nr bank -> I get two results transcripts that have matches against nr bank (potential protein) and those who have not matches
2 / Translate my two previous files protein sequences with prodigal -> I sort the complete ORF ( start + stop codon ) and incomplete
3 / search the secretion signal with signalP and secretomeP -> I get the potential secretome with an annotated file and another non annotated
4 / secretome annotated and unannotated secretome I can make a InterProScan for information on protein motifs.
The question I ask myself is it not better than me to do the translation from the start , then make a BLASTP on the translated protein sequences because maybe the translation into protein sequence does not give quite the same result the BLASTX ?
Thanks for your help
