mkESA: enhanced suffix array construction tool.
Where this comes from
- Record sourced from PubMed, PMID 19246510.
- Also identified by DOI 10.1093/bioinformatics/btp112 and PMC identifier 2666816.
- Licence recorded as CC BY-NC.
- Because redistribution is not established, this page shows the abstract only. Follow the links below for the full text.
Abstract
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.
Medical subject headings
- Algorithms
- Computational Biology
- Sequence Analysis
- Software