I fully agree with Mathew. Blast is the tool to use. Use a strict enough e value, set the number of descriptions to 1 and number of alignment to O, otherwise you will be flooded with redundant results
Yes, search for perfect BLAST hits of these 4000 proteins against your transcriptome of interest. Let us know if you face any problems as it is quite easy to perform.
Thank you for your approaches. We tried with Blast but the reference transcriptome that we want to compare with our data doesn't appear in the database. We could not download Blast plus either. If you know about any guidelines or tutorial please let me know. Thank you!