mkESA: enhanced suffix array construction tool

Abstract

Summary: We introduce the tool mkESA, an open source program for constructing enhanced suffix arrays (ESAs), striving for low memory consumption, yet high practical speed. mkESA is a user-friendly program written in portable C99, based on a parallelized version of the Deep-Shallow suffix array construction algorithm, which is known for its high speed and small memory usage. The tool handles large FASTA files with multiple sequences, and computes suffix arrays and various additional tables, such as the LCP table (longest common prefix) or the inverse suffix array, from given sequence data.Availability: The source code of mkESA is freely available under the terms of the GNU General Public License (GPL) version 2 at http://bibiserv.techfak.uni-bielefeld.de/mkesa/.Contact: rhomann@techfak.uni-bielefeld.de

Parallel lightweight wavelet tree, suffix array and FM-index construction

“…These algorithms first construction the BWT over parts of the input and then merge these parts in parallel. Many bioinformatics applications use compressed SA, thus there are frameworks with parallel SACA implementations especially optimized for DNA input [Lea13,Hea09]. For example, PASQUAL [Lea13] has a fast implementation using a combination of prefix doubling and string sorting algorithms.…”

Parallel distributed memory construction of suffix and longest common prefix arrays

“…Some shared memory algorithms and implementations have been proposed. Homann et al [13] introduced the mkESA algorithm, which is a parallelized variant of the Deep-Shallow algorithm of Manzini and Ferragina [23]. The authors of mkESA report a speedup of less than 2 when using 16 threads.…”

“…The divsufsort suffix array implementation [25] serves as the sequential comparison, since it is open source and is known as one of the fastest and lightweight suffix array construction implementations. Furthermore, we run the shared-memory parallel suffix array and LCP construction tool mkESA [13]. Additionally, we directly compare our implementation with the FAK implementation cloudSACA by Abdelhadi et al [1].…”

To Detect and Analyze Sequence Repeats Whatever Be Their Origin

“…In the current state of the art, the best structure is the suffix array, a simple list of starting positions in a sequence sorted according to the ascending lexicographical order of each corresponding subsequence. For instance the suffix array of sequence GTTCGTTTCTTA is [12,4,9,1,5,11,3,8,10,2,7,6] 9showing that suffix arrays can replace suffix trees in every aspect. In practice, some additional pre-computed tables are necessary towards this aim -based on explicit recording of prefixes common to two consecutive entries in the array-, a minor change with respect to the main structure.…”

“…As for suffix trees, suffix array can be built with a linear time and space complexity. The best implementation available to date is probably SAIS, which has been conceived by G. which answers all these constraints (12). Its output is compatible with mkvtree, another widely used implementation included in the package Vmatch ( 9, see section 3).…”