1. A method of matching a query sequence in a weighted-sequences index, comprising: receiving a query sequence comprising symbols; transforming the query sequence into a weighted query sequence comprising the symbols and corresponding weights; reordering the weighted query sequence such that the symbols that occur less frequency are ordered earlier than the symbols that occur more frequently; encoding the re-ordered weighted query sequence into a one-dimensional sequence; and searching an iso-depth link of the weighted-sequences index using the one-dimensional sequence to return an offset.