دورية أكاديمية
Concurrent and Accurate Short Read Mapping on Multicore Processors
| العنوان: | Concurrent and Accurate Short Read Mapping on Multicore Processors |
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| المؤلفون: | Martínez Pérez, Héctor, Tárraga, Joaquín, Medina, Ignacio, Barrachina Mir, Sergio, Castillo Catalán, María Isabel, Dopazo, Joaquín, Quintana-Orti, Enrique S. |
| بيانات النشر: | IEEE |
| سنة النشر: | 2016 |
| المجموعة: | Repositori Universitat Jaume I (Repositorio UJI) |
| مصطلحات موضوعية: | RNA, Short-read alignment, Suffix array search, Smith-Waterman’s algorithm, High performance computing, Multicore processors |
| الوصف: | We introduce a parallel aligner with a work-flow organization for fast and accurate mapping of RNA sequences on servers equipped with multicore processors. Our software, HPG Aligner SA1, exploits a suffix array to rapidly map a large fraction of the RNA fragments (reads), as well as leverages the accuracy of the Smith-Waterman algorithm to deal with conflictive reads. The aligner is enhanced with a careful strategy to detect splice junctions based on an adaptive division of RNA reads into small segments (or seeds), which are then mapped onto a number of candidate alignment locations, providing crucial information for the successful alignment of the complete reads. The experimental results on a platform with Intel multicore technology report the parallel performance of HPG Aligner SA, on RNA reads of 100–400 nucleotides, which excels in execution time/sensitivity to state-of-the-art aligners such as TopHat 2+Bowtie 2, MapSplice, and STAR. ; This work has been supported by the Bull-CIPF Chair for Computational Genomics. The researchers from the Jaume I University were supported by project TIN2011-23283 and FEDER. |
| نوع الوثيقة: | article in journal/newspaper |
| وصف الملف: | application/pdf |
| اللغة: | English |
| تدمد: | 1545-5963 |
| العلاقة: | IEEE/ACM Transactions on, 2015, vol. 12, no 5; http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=7010005&tag=1Test; MARTINEZ, Hector, et al. Concurrent and Accurate Short Read Mapping on Multicore Processors. Computational Biology and Bioinformatics, IEEE/ACM Transactions on, 2015, vol. 12, no 5, p. 995-1007.; http://hdl.handle.net/10234/154007Test; http://dx.doi.org/10.1109/TCBB.2015.2392077Test |
| DOI: | 10.1109/TCBB.2015.2392077 |
| الإتاحة: | https://doi.org/10.1109/TCBB.2015.2392077Test http://hdl.handle.net/10234/154007Test |
| حقوق: | © Copyright 2016 IEEE - All rights reserved. ; http://rightsstatements.org/vocab/InC/1.0Test/ ; info:eu-repo/semantics/openAccess |
| رقم الانضمام: | edsbas.D1159F2B |
| قاعدة البيانات: | BASE |
| تدمد: | 15455963 |
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| DOI: | 10.1109/TCBB.2015.2392077 |