A bioinformatician's guide to the forefront of suffix array construction algorithms
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 Di...
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| Published in | Briefings in bioinformatics Vol. 15; no. 2; pp. 138 - 154 |
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| Main Authors | , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Oxford Publishing Limited (England)
01.03.2014
Oxford University Press |
| Subjects | |
| Online Access | Get full text |
| ISSN | 1467-5463 1477-4054 1477-4054 |
| DOI | 10.1093/bib/bbt081 |
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| 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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| AbstractList | 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. 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. [PUBLICATION 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.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. |
| Author | Shrestha, A. M. S. Frith, M. C. Horton, P. |
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| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/24413184$$D View this record in MEDLINE/PubMed |
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| Keywords | subset seeds text index spaced seeds suffix array construction linear-time algorithm |
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| Title | A bioinformatician's guide to the forefront of suffix array construction algorithms |
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