Knowing nothing about Bioperl, you could take the following approach

• Iterate through the file while (<$FILE_HANDLE>){
• split each line on space. @record=split(/ /,$_);
• if it consists of two integers ignore
• if not join the record elements from 1 to $#record join ('',@record[1..$#record])
• concatenate the resulting string onto $hash{$record[0]}
• use substr to find the character at a specific index in each sequence for my $sequence (keys (%hash))

See how far that takes you along the path and let us know if you're stuck, no need to apologise we like to help.