I know this might sound like a really basic question for some, but I'm a very beginner in bioinformatics and sequence analysis..
So, I ran blastn on NCBI-BLAST on an RNA sequence to which I intend to predict the secondary structure.. The output of the BLAST contains some sequences that are labeled "plus/plus" and some that are labeled "plus/minus"..
My question is: my next step should be multiple sequence alignment.. Should I flip the "minus" subject sequences so all the sequences in the MSA input are in the same orientation, or should I run MSA on the BLAST output sequences as they are?
Thanks in advance!