Fractal MapReduce decomposition of sequence alignment

Bibliographic Details
Main Author: Almeida, Jonas S.
Publication Date: 2012
Other Authors: Grüneberg, Alexander, Maass,  Wolfgang, Vinga, Susana
Format: Article
Language: eng
Source: Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
Download full: http://hdl.handle.net/10362/23600
Summary: 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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spelling 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/10362/23600engPURE: 400511https://doi.org/10.1186/1748-7188-7-12info:eu-repo/semantics/openAccessreponame:Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)instname:FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologiainstacron:RCAAP2024-06-10T01:43:45Zoai:run.unl.pt:10362/23600Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireinfo@rcaap.ptopendoar:https://opendoar.ac.uk/repository/71602025-05-28T16:59:07.565740Repositórios Científicos de Acesso Aberto de Portugal (RCAAP) - FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologiafalse
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 PURE: 400511
https://doi.org/10.1186/1748-7188-7-12
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:Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
instname:FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
instacron:RCAAP
instname_str FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
instacron_str RCAAP
institution RCAAP
reponame_str Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
collection Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
repository.name.fl_str_mv Repositórios Científicos de Acesso Aberto de Portugal (RCAAP) - FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
repository.mail.fl_str_mv info@rcaap.pt
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