Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis

Detalhes bibliográficos
Autor(a) principal: Vinga, Susana
Data de Publicação: 2012
Outros Autores: Carvalho,  Alexandra M, Francisco, Alexandre P, Russo,  Luis M S, Almeida,  Jonas S
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10362/23351
Resumo: This work was partially supported by FCT through the PIDDAC Program funds (INESC-ID multiannual funding) and under grant PEst-OE/EEI/LA0008/2011 (IT multiannual funding). In addition, it was also partially funded by projects HIVCONTROL (PTDC/EEA-CRO/100128/2008, S. Vinga, PI), TAGS (PTDC/EIA-EIA/112283/2009) and NEUROCLINOMICS (PTDC/EIA-EIA/111239/2009) from FCT (Portugal).
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spelling Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysisTANDEM REPEATSDNA-SEQUENCESGENOMIC SIGNATURETREESULTRAFASTEFFICIENT ALIGNMENTALGORITHMSHORT READ ALIGNMENTCLASSIFICATIONSEARCHSHORT READ ALIGNMENTDNA-SEQUENCESGENOMIC SIGNATUREEFFICIENT ALIGNMENTTANDEM REPEATSCLASSIFICATIONALGORITHMULTRAFASTSEARCHTREESThis work was partially supported by FCT through the PIDDAC Program funds (INESC-ID multiannual funding) and under grant PEst-OE/EEI/LA0008/2011 (IT multiannual funding). In addition, it was also partially funded by projects HIVCONTROL (PTDC/EEA-CRO/100128/2008, S. Vinga, PI), TAGS (PTDC/EIA-EIA/112283/2009) and NEUROCLINOMICS (PTDC/EIA-EIA/111239/2009) from FCT (Portugal).Background: Chaos Game Representation (CGR) is an iterated function that bijectively maps discrete sequences into a continuous domain. As a result, discrete sequences can be object of statistical and topological analyses otherwise reserved to numerical systems. Characteristically, CGR coordinates of substrings sharing an L-long suffix will be located within 2(-L) distance of each other. In the two decades since its original proposal, CGR has been generalized beyond its original focus on genomic sequences and has been successfully applied to a wide range of problems in bioinformatics. This report explores the possibility that it can be further extended to approach algorithms that rely on discrete, graph-based representations. Results: The exploratory analysis described here consisted of selecting foundational string problems and refactoring them using CGR-based algorithms. We found that CGR can take the role of suffix trees and emulate sophisticated string algorithms, efficiently solving exact and approximate string matching problems such as finding all palindromes and tandem repeats, and matching with mismatches. The common feature of these problems is that they use longest common extension (LCE) queries as subtasks of their procedures, which we show to have a constant time solution with CGR. Additionally, we show that CGR can be used as a rolling hash function within the Rabin-Karp algorithm. Conclusions: The analysis of biological sequences relies on algorithmic foundations facing mounting challenges, both logistic (performance) and analytical (lack of unifying mathematical framework). CGR is found to provide the latter and to promise the former: graph-based data structures for sequence analysis operations are entailed by numerical-based data structures produced by CGR maps, providing a unifying analytical framework for a diversity of pattern matching problems.NOVA Medical School|Faculdade de Ciências Médicas (NMS|FCM)RUNVinga, SusanaCarvalho,  Alexandra MFrancisco, Alexandre PRusso,  Luis M SAlmeida,  Jonas S2017-09-18T22:01:05Z2012-05-022012-05-02T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article12application/pdfhttp://hdl.handle.net/10362/23351eng1748-7188PURE: 401206https://doi.org/10.1186/1748-7188-7-10info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2024-03-11T04:11:36Zoai:run.unl.pt:10362/23351Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T03:27:46.018841Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis
title Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis
spellingShingle Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis
Vinga, Susana
TANDEM REPEATS
DNA-SEQUENCES
GENOMIC SIGNATURE
TREES
ULTRAFAST
EFFICIENT ALIGNMENT
ALGORITHM
SHORT READ ALIGNMENT
CLASSIFICATION
SEARCH
SHORT READ ALIGNMENT
DNA-SEQUENCES
GENOMIC SIGNATURE
EFFICIENT ALIGNMENT
TANDEM REPEATS
CLASSIFICATION
ALGORITHM
ULTRAFAST
SEARCH
TREES
title_short Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis
title_full Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis
title_fullStr Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis
title_full_unstemmed Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis
title_sort Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis
author Vinga, Susana
author_facet Vinga, Susana
Carvalho,  Alexandra M
Francisco, Alexandre P
Russo,  Luis M S
Almeida,  Jonas S
author_role author
author2 Carvalho,  Alexandra M
Francisco, Alexandre P
Russo,  Luis M S
Almeida,  Jonas S
author2_role author
author
author
author
dc.contributor.none.fl_str_mv NOVA Medical School|Faculdade de Ciências Médicas (NMS|FCM)
RUN
dc.contributor.author.fl_str_mv Vinga, Susana
Carvalho,  Alexandra M
Francisco, Alexandre P
Russo,  Luis M S
Almeida,  Jonas S
dc.subject.por.fl_str_mv TANDEM REPEATS
DNA-SEQUENCES
GENOMIC SIGNATURE
TREES
ULTRAFAST
EFFICIENT ALIGNMENT
ALGORITHM
SHORT READ ALIGNMENT
CLASSIFICATION
SEARCH
SHORT READ ALIGNMENT
DNA-SEQUENCES
GENOMIC SIGNATURE
EFFICIENT ALIGNMENT
TANDEM REPEATS
CLASSIFICATION
ALGORITHM
ULTRAFAST
SEARCH
TREES
topic TANDEM REPEATS
DNA-SEQUENCES
GENOMIC SIGNATURE
TREES
ULTRAFAST
EFFICIENT ALIGNMENT
ALGORITHM
SHORT READ ALIGNMENT
CLASSIFICATION
SEARCH
SHORT READ ALIGNMENT
DNA-SEQUENCES
GENOMIC SIGNATURE
EFFICIENT ALIGNMENT
TANDEM REPEATS
CLASSIFICATION
ALGORITHM
ULTRAFAST
SEARCH
TREES
description This work was partially supported by FCT through the PIDDAC Program funds (INESC-ID multiannual funding) and under grant PEst-OE/EEI/LA0008/2011 (IT multiannual funding). In addition, it was also partially funded by projects HIVCONTROL (PTDC/EEA-CRO/100128/2008, S. Vinga, PI), TAGS (PTDC/EIA-EIA/112283/2009) and NEUROCLINOMICS (PTDC/EIA-EIA/111239/2009) from FCT (Portugal).
publishDate 2012
dc.date.none.fl_str_mv 2012-05-02
2012-05-02T00:00:00Z
2017-09-18T22:01:05Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10362/23351
url http://hdl.handle.net/10362/23351
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv 1748-7188
PURE: 401206
https://doi.org/10.1186/1748-7188-7-10
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 12
application/pdf
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
institution RCAAP
reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
repository.mail.fl_str_mv
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