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Related Experiment Video

Updated: Jun 25, 2026

Fabrication and Use of MicroEnvironment microArrays (MEArrays)

Fabrication and Use of MicroEnvironment microArrays (MEArrays)

Published on: October 11, 2012

mkESA: enhanced suffix array construction tool.

Robert Homann¹, David Fleer, Robert Giegerich

¹International NRW Graduate School in Bioinformatics and Genome Research, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany. rhomann@techfak.uni-bielefeld.de

Bioinformatics (Oxford, England)

|February 28, 2009

Summary

mkESA is a new open-source tool for constructing enhanced suffix arrays (ESAs) efficiently. It offers low memory use and high speed for analyzing large FASTA files and generating essential sequence data tables.

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Area of Science:

Bioinformatics
Computational Biology
Data Structures

Background:

Suffix array construction is crucial for sequence analysis.
Existing methods often face challenges with memory consumption or speed.
Efficient tools are needed for handling large genomic datasets.

Purpose of the Study:

To introduce mkESA, an open-source program for enhanced suffix array (ESA) construction.
To provide a tool that balances low memory usage with high practical speed.
To facilitate the analysis of large FASTA files with multiple sequences.

Main Methods:

Developed mkESA using portable C99.
Implemented a parallelized version of the Deep-Shallow suffix array construction algorithm.
The tool is designed for user-friendliness and efficiency.

Main Results:

mkESA achieves low memory consumption and high practical speed.
The program successfully constructs enhanced suffix arrays (ESAs).
It computes additional tables like the LCP table and inverse suffix array.

Conclusions:

mkESA is an efficient and user-friendly tool for constructing enhanced suffix arrays.
It addresses the need for memory-efficient and fast sequence data analysis.
The tool supports the generation of multiple essential bioinformatics tables from FASTA files.