## Do I provide the key for the hash as soon as I read in the line bearing the sequence name?

No, you've already 'created' the key in the hash by assigning a value to it with $HoA_sequences{$line} =

Are you using Data::Dumper or similar and liberally placed debug print statements to see what is going on with your data structure? I recommend creating a simple dummy data set and doing lots of trial and error and debug printing. Much more effective than any other method of learning this stuff.

## And can I create a hash with a key but no hash? I'm guessing not. :/

If you mean "a key with no value", sure you can.

my %hash = ( foo => 'bar', baz => '', qux => undef );
[download]

Now print that with Data::Dumper and see what it looks like.

## Once captured how do I continue to the next line to query if ...

See the flip-flop operator for one way.

Update: added link and examples