Search through the website, there are many similar scenarios that you can learn and develop your approach from, we really value folks trying to do their part and then when they're spent for resources they come and ask for directions/opinions/approaches, this way the learning process can become more interactive and lasting. I could get you the following links to nodes posted withing the Monastery to get you started, these are replete in discussions covering the basic areas of the functionality your seek .
Soon as you are able to read a file then you can do many things with the lines that you read involving creating hashes. Here in your situation, you have two ways to go, you can either directly use Perl or use BioPerl, the later offers - at the price of time - good libraries to manipulate sequences in a systematic way...
in reply to Hash help for biologist
Try your best and we are ready to pitch in as soon as you do your part on the side of learning...
Excellence is an Endeavor of Persistence.
A Year-Old Monk :D .