I have a file on a server on another campus that's all in lowercase that i need to changed to all uppercase. Is there any simple unix command that will do this? [i'm using PuTTy on a PC if that makes any difference.]

It's only 4 different letters (it's DNA, so just A, T, C, and G) so 4 separate search and replace functions would also work. (In VI or another text editor which will work through remote access.) but i don't know how to do a search and replace in VI? 

I could copy it to my desktop, do a search and replace in a local text editor and then copy back, but then it would end up full of windows line breaks? [i'm on a PC, the remote machine is a linux server, and the program i need to interpret the DNA file can only handle unix line breaks.]