Fractal MapReduce decomposition of sequence alignment
| Autor(a) principal: | |
|---|---|
| Data de Publicação: | 2012 |
| Outros Autores: | , , |
| Tipo de documento: | Artigo |
| Idioma: | eng |
| Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
| Texto Completo: | http://hdl.handle.net/10362/23600 |
Resumo: | This work was supported in part by the Center for Clinical and Translational Sciences of the University of Alabama at Birmingham under contract no. 5UL1 RR025777-03 from NIH National Center for Research Resources, by the National Cancer Institute grant 1U24CA143883-01, by the European Union FP7 PNEUMOPATH (HEALTH F3 2009 222983). |
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Fractal MapReduce decomposition of sequence alignmentMAPSCHAOS GAME REPRESENTATIONFRAMEWORKBIOLOGICAL SEQUENCESThis work was supported in part by the Center for Clinical and Translational Sciences of the University of Alabama at Birmingham under contract no. 5UL1 RR025777-03 from NIH National Center for Research Resources, by the National Cancer Institute grant 1U24CA143883-01, by the European Union FP7 PNEUMOPATH (HEALTH F3 2009 222983).Background: The dramatic fall in the cost of genomic sequencing, and the increasing convenience of distributed cloud computing resources, positions the MapReduce coding pattern as a cornerstone of scalable bioinformatics algorithm development. In some cases an algorithm will find a natural distribution via use of map functions to process vectorized components, followed by a reduce of aggregate intermediate results. However, for some data analysis procedures such as sequence analysis, a more fundamental reformulation may be required. Results: In this report we describe a solution to sequence comparison that can be thoroughly decomposed into multiple rounds of map and reduce operations. The route taken makes use of iterated maps, a fractal analysis technique, that has been found to provide a "alignment-free" solution to sequence analysis and comparison. That is, a solution that does not require dynamic programming, relying on a numeric Chaos Game Representation (CGR) data structure. This claim is demonstrated in this report by calculating the length of the longest similar segment by inspecting only the USM coordinates of two analogous units: with no resort to dynamic programming. Conclusions: The procedure described is an attempt at extreme decomposition and parallelization of sequence alignment in anticipation of a volume of genomic sequence data that cannot be met by current algorithmic frameworks. The solution found is delivered with a browser-based application (webApp), highlighting the browser's emergence as an environment for high performance distributed computing. Availability: Public distribution of accompanying software library with open source and version control at http://usm.github.com. Also available as a webApp through Google Chrome's WebStore http://chrome.google.com/webstore: search with "usm".NOVA Medical School|Faculdade de Ciências Médicas (NMS|FCM)RUNAlmeida, Jonas S.Grüneberg, AlexanderMaass, WolfgangVinga, Susana2017-09-26T13:47:06Z2012-052012-05-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article12application/pdfhttp://hdl.handle.net/10362/23600eng1748-7188PURE: 400511https://doi.org/10.1186/1748-7188-7-12info: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:RCAAP2024-03-11T04:11:54Zoai:run.unl.pt:10362/23600Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T03:27:51.048542Repositório 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 |
Fractal MapReduce decomposition of sequence alignment |
| title |
Fractal MapReduce decomposition of sequence alignment |
| spellingShingle |
Fractal MapReduce decomposition of sequence alignment Almeida, Jonas S. MAPS CHAOS GAME REPRESENTATION FRAMEWORK BIOLOGICAL SEQUENCES |
| title_short |
Fractal MapReduce decomposition of sequence alignment |
| title_full |
Fractal MapReduce decomposition of sequence alignment |
| title_fullStr |
Fractal MapReduce decomposition of sequence alignment |
| title_full_unstemmed |
Fractal MapReduce decomposition of sequence alignment |
| title_sort |
Fractal MapReduce decomposition of sequence alignment |
| author |
Almeida, Jonas S. |
| author_facet |
Almeida, Jonas S. Grüneberg, Alexander Maass, Wolfgang Vinga, Susana |
| author_role |
author |
| author2 |
Grüneberg, Alexander Maass, Wolfgang Vinga, Susana |
| author2_role |
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 |
Almeida, Jonas S. Grüneberg, Alexander Maass, Wolfgang Vinga, Susana |
| dc.subject.por.fl_str_mv |
MAPS CHAOS GAME REPRESENTATION FRAMEWORK BIOLOGICAL SEQUENCES |
| topic |
MAPS CHAOS GAME REPRESENTATION FRAMEWORK BIOLOGICAL SEQUENCES |
| description |
This work was supported in part by the Center for Clinical and Translational Sciences of the University of Alabama at Birmingham under contract no. 5UL1 RR025777-03 from NIH National Center for Research Resources, by the National Cancer Institute grant 1U24CA143883-01, by the European Union FP7 PNEUMOPATH (HEALTH F3 2009 222983). |
| publishDate |
2012 |
| dc.date.none.fl_str_mv |
2012-05 2012-05-01T00:00:00Z 2017-09-26T13:47:06Z |
| 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/10362/23600 |
| url |
http://hdl.handle.net/10362/23600 |
| dc.language.iso.fl_str_mv |
eng |
| language |
eng |
| dc.relation.none.fl_str_mv |
1748-7188 PURE: 400511 https://doi.org/10.1186/1748-7188-7-12 |
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info:eu-repo/semantics/openAccess |
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openAccess |
| dc.format.none.fl_str_mv |
12 application/pdf |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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RCAAP |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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