Suffix Array - Construction Algorithms

Construction Algorithms

A naive approach to construct a suffix array is to use a comparison-based sorting algorithm. These algorithms require suffix comparisons, but a suffix comparison runs in time, so the overall runtime of this approach is .

More advanced algorithms take advantage of the fact that the suffixes to be sorted are not arbitrary strings but related to each other. These algorithms strive to achieve the following goals:

• minimal asymptotic complexity
• lightweight in space, meaning little or no working memory beside the text and the suffix array itself is needed
• fast in practice

One of the first algorithms to achieve all goals is the SA-IS algorithm of Nong, Zhang & Chan (2009). The algorithm is also rather simple (< 100 LOC) and can be enhanced to simultaneously construct the LCP array. The SA-IS algorithm is one of the fastest known suffix array construction algorithms. A careful implementation by Yuta Mori outperforms most other linear or super-linear construction approaches.

Beside time and space requirements, suffix array construction algorithms are also differentiated by their supported alphabet: constant alphabets where the alphabet size is bound by a constant, integer alphabets where characters are integers in a range depending on and general alphabets where only character comparisons are allowed.

Most suffix array construction algorithms are based on one of the following approaches:

• Prefix doubling algorithms are based on a strategy of Karp, Miller & Rosenberg (1972). The idea is to find prefixes that honor the lexicographic ordering of suffixes. The assessed prefix length doubles in each iteration of the algorithm until a prefix is unique and provides the rank of the associated suffix.
• Recursive algorithms follow the approach of the suffix tree construction algorithm by Farach (1997) to recursively sort a subset of suffixes. This subset is then used to infer a suffix array of the remaining suffixes. Both of these suffix arrays are then merged to compute the final suffix array.
• Induced copying algorithms are similar to recursive algorithms in the sense that they use an already sorted subset to induce a fast sort of the remaining suffixes. The difference is that these algorithms favor iteration over recursion to sort the selected suffix subset. A survey of this diverse group of algorithms has been put together by Puglisi, Smyth & Turpin (2007).

A well-known recursive algorithm for integer alphabets is the DC3 / skew algorithm of Kärkkäinen & Sanders (2003). It runs in linear time and has successfully been used as the basis for parallel and external memory suffix array construction algorithms.

Recent work by Salson et al. (2009) proposes an algorithm for updating the suffix array of a text that has been edited instead of rebuilding a new suffix array from scratch. Even if the theoretical worst-case time complexity is, it appears to perform well in practice: experimental results from the authors showed that their implementation of dynamic suffix arrays is generally more efficient than rebuilding when considering the insertion of a reasonable number of letters in the original text.