I am new to bioinformatics. I am trying to find complementarity between mRNAs and rRNAs.
Precisely, I have a list of 5'UTR mRNAs and I want to find the mRNAs that have complementarity as long as at least 5 nucleotide with a specific rRNA (say 18S).
Since as far as I understood, web BLAST just gives the similar sequences and not the complementary sequences, I got the reverse-complementary sequence of 18S rRNA and pasted that to the query section of BLAST. I also had a .fasta file containing the 5'UTR mRNAs which I could upload to the BLAST web page. But every time I do this (in blastn) I receive a "Bad gateway" error (Error 502) .
I have two questions here:
Why am I receiving this error?
How can I specify that I just want 5 similar nucleotide (between mRNAs and rRNA) in the sequence? Is it possible at all using BLAST?
Thank you very much!