1. A method of matching a query sequence in a weighted-sequences index, comprising: transforming a query sequence comprising symbols into a weighted query sequence comprising a sequence of pairs, wherein each pair includes a corresponding one of the symbols and a corresponding weight, and wherein the corresponding weight is represented by a real number; reordering the weighted query sequence such that the pairs having symbols that occur less frequently in the weighted query sequence are ordered earlier than the pairs having symbols that occur more frequently; encoding the re-ordered pairs of the weighted query sequence into a one-dimensional sequence comprising encoded symbols, wherein each encoded symbol includes a symbol of a corresponding first one of the re-ordered pairs and a weight parameter that is a difference between the weight of the symbol and a weight of a second one of the re-ordered pairs that is adjacent the first re-ordered pair; and searching an iso-depth link of the weighted-sequences index using the one-dimensional sequence to return an offset.