@brainstorm 
Well, I don't know if it is a standard procedure for major sequence alignment/ classification tool. 
There is certain difference between Capital letter and lower letter right? Lower letter is for RNA right? 
Even if it is needed. I assume most of query data are genome data, thus maybe we should just do a 'tocapital' process instead?

Let me know if it is mandatory, in that case, I ll just switch it back