ArticleBriefings in bioinformatics2014
A bioinformatician's guide to the forefront of suffix array construction algorithms.
Article in Briefings in bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Article
- Graphite: painting genomes using a colored de Bruijn graph.NAR genomics and bioinformatics · 2024Article
- Fast, parallel, and cache-friendly suffix array construction.Algorithms for molecular biology : AMB · 2024Article
- Lightweight Pattern Matching Method for DNA Sequencing in Internet of Medical Things.Computational intelligence and neuroscience · 2022Article
- Establishment of a polymerase chain reaction-based method for strain-level management ofFrontiers in microbiology · 2022Article
- The Utility of Data Transformation for Alignment, De Novo Assembly and Classification of Short Read Virus Sequences.Viruses · 2019Article
- RIblast: an ultrafast RNA-RNA interaction prediction system based on a seed-and-extension approach.Bioinformatics (Oxford, England) · 2017Article
- Two Efficient Techniques to Find Approximate Overlaps between Sequences.BioMed research international · 2017Article
- Best hits of 11110110111: model-free selection and parameter-free sensitivity calculation of spaced seeds.Algorithms for molecular biology : AMB · 2017Article
- Defining rules of CD8(+) T cell expansion against pre-erythrocytic Plasmodium antigens in sporozoite-immunized mice.Malaria journal · 2016Article
- Article
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The suffix array and its variants are text-indexing data structures that have become indispensable in the field of bioinformatics. With the uninitiated in mind, we provide an accessible exposition of the SA-IS algorithm, which is the state of the art in suffix array construction. We also describe DisLex, a technique that allows standard suffix array construction algorithms to create modified suffix arrays designed to enable a simple form of inexact matching needed to support 'spaced seeds' and 'subset seeds' used in many biological applications.
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