My PI gave me a list of some DNA sequences, each one around 25 nucleotides, that are suspected to code for Vitis Vitinesfera miRNA. To know if they are complementary to some mRNA for a known protein sequence, we do the following process:
- BLAST the sequence against a nucleotide database of Vitis Vinifera (TSA database)
- Take some of the results and using their accession number BLASTX against a database of Vitis Vinifera (or related organisms) proteins (nr database).
Combining the results of 1 and 2, if any in both cases, we can know if the initial sequence is complementary to the mRNA of some known protein.
My PI wants me to automate this process, probably through writing a program.
This is my first contact with bioinformatics and is being of great learning value to me since I learned about Blast, Blast+, Biopython, etc. and I believe that I am arriving at a reasonable way to at least partially automate it.
Yet, this seems to be a problem so simple and so easy to come across that I find it hard to believe that there aren't any readily available solutions. I would like to ask if you know some program, or website, that does that or what would be the best way to arrive at such a solution.