if the header is always that format, then you wouldn't need to store the whole header, as it just becomes a contiguous sequence of increasing integers...and hence $Sequences[1] is already known to be for header "Seq1" implicitly. And if the headers are not that straight forth, then depending exactly on the processing required, probably opt for a hash of array or array of hashes, which keeps the header directly tied to the sequence, rather than separate header and separate sequence data structures.