in reply to Searching and Parsing Biological data

This is a common operation which perl is will suited for. Whenever you want to look read in one file and look up associated information in another file, it will involve using a hash to "index" the second file so you can find the information quickly. The basic recipe is:
for each line of the second file: parse it and locate the key store the second line in a hash indexed by its key endfor for each line of the first file: parse it and locate its common key with the second file look up the associated line using the hash do something with both lines endfor
Examples of how to do each of these steps can be found in these nodes:
Re: Combine files, while parsing info. (see the example in the <readmore> section
Re: compare data between two files using Perl

Your problem is complicated by the fact that you have several files you want to "join" together, but the basic approach won't change. This is similar to a "relational join" operation between tables in database parlance.