Shell Programming and Scripting

Dear all,
I'm very new in scripting and using shell and prompt command.
I have a program (called fasta) and I need to iterate it over all files in a folder, but I'm not able to do that. Pratically the fasta program wants a sintax like this:

fasta.exe [option] query_file.txt library_file.txt > output_file

I need to iterate this command over the files in a folder.
Any suggestion, advice or help is kindly needed!
Thank you in advance!
Gab

Code:

for %a in (*.txt) DO echo %%a

Note that it's extremely difficult to do complex things inside this kind of loop, the for syntax being somewhat of an afterthought, badly stapled to the side of CMD syntax after the fact. Hopefully sufficient for your needs.

Thank you anyway...I think that my command is too complicate to be iterated only by a for cycle.