Felipe Alves da Louza

External Memory Generalized Suffix and LCP Arrays Construction

A suffix array is a data structure that, together with the LCP array, allows solving many string processing problems in a very efficient fashion. In this article we introduce eGSA, the first external memory algorithm to construct both generalized suffix and LCP arrays for sets of strings. Our algorithm relies on a combination of buffers, induced sorting and a heap. Performance tests with real DNA sequence sets of size up to 8.5 GB showed that eGSA can indeed be applied to sets of large sequences with efficient running time on a low-cost machine. Compared to the algorithm that most closely resembles eGSA purpose, eSAIS, eGSA reduced the time spent to construct the arrays by a factor of 2.5−4.8.

Induced Suffix Sorting for String Collections

Sorting all suffixes of a string collection may be performed by sorting the concatenation of all strings using different end marker symbols as separators, or alternatively using the same end marker as separator. However, both approaches have the following drawbacks. The first alternative increases the alphabet size of the resulting string by the number of strings, whereas the second alternative does not guarantee the order among suffixes that are equal up to the end marker symbol. In this article, we show how to modify two important suffix sorting algorithms, SAIS [1] and SACA-K [2], to sort the concatenated string using the same end marker, maintaining their theoretical bounds, respecting the order among all suffixes, and improving their practical performance.

Generalized enhanced suffix array construction in external memory

BackgroundSuffix arrays, augmented by additional data structures, allow solving efficiently many string processing problems. The external memory construction of the generalized suffix array for a string collection is a fundamental task when the size of the input collection or the data structure exceeds the available internal memory.ResultsIn this article we present and analyze

Computing Burrows-Wheeler Similarity Distributions for String Collections

\mathsf {eGSA}

Time Series Indexing Taking Advantage of the Generalized Suffix Tree

eGSA [introduced in CPM (External memory generalized suffix and

A Grammar Compression Algorithm Based on Induced Suffix Sorting

\mathsf {LCP}