Comparative analysis of protein alignment algorithms in parallel environment using CUDA
Cataloged from PDF version of thesis report.
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BRAC University
2016
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| גישה מקוונת: | http://hdl.handle.net/10361/5405 |
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10361-54052022-01-26T10:19:59Z Comparative analysis of protein alignment algorithms in parallel environment using CUDA Fahim, Shadman Prince, Gulshan Jubaed Hossain, Shehabul Uddin, Jia Department of Computer Science and Engineering, BRAC University Computer science and engineering CSE Cataloged from PDF version of thesis report. Includes bibliographical references (page 44-45). This thesis report is submitted in partial fulfillment of the requirements for the degree of Bachelor of Science in Computer Science and Engineering, 2016. In bioinformatics to identify evolutionary relationships two sequences are matched to find similarity. Smith Waterman, a dynamic algorithm, is a common choice to carry out this alignment process. However, with the exponential growth of protein databases this algorithm’s time complexity increases. The demand of bioinformatics for their tasks to speed up is very high. Even a slight seed up in computation would be very helpful in the field of bioinformatics. Thus, for a lot of the scientists this algorithm might not be the first choice. In today’s world the most popular and used bioinformatics tool is the BLAST (Basic Local Alignment Tool). BLAST, similar to Smith Waterman algorithm, is an alignment algorithm for scanning proteins from protein databases. This thesis analyzes both the algorithms in a parallel environment with the help of NVIDIA GPU. For our experiments we utilized a GeForce GTX 660 NVIDIA GPU to execute both the algorithms. Experimental results show that BLAST is on average is 2.5 times faster than Smith-Waterman. Shadman Fahim Gulshan Jubaed Prince Shehabul Hossain B. Computer Science and Engineering 2016-05-29T11:36:48Z 2016-05-29T11:36:48Z 2016 4/18/2016 Thesis ID 12301011 ID 12301014 ID 12301005 http://hdl.handle.net/10361/5405 en BRAC University thesis are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. 45 pages application/pdf BRAC University |
| institution |
Brac University |
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Institutional Repository |
| language |
English |
| topic |
Computer science and engineering CSE |
| spellingShingle |
Computer science and engineering CSE Fahim, Shadman Prince, Gulshan Jubaed Hossain, Shehabul Comparative analysis of protein alignment algorithms in parallel environment using CUDA |
| description |
Cataloged from PDF version of thesis report. |
| author2 |
Uddin, Jia |
| author_facet |
Uddin, Jia Fahim, Shadman Prince, Gulshan Jubaed Hossain, Shehabul |
| format |
Thesis |
| author |
Fahim, Shadman Prince, Gulshan Jubaed Hossain, Shehabul |
| author_sort |
Fahim, Shadman |
| title |
Comparative analysis of protein alignment algorithms in parallel environment using CUDA |
| title_short |
Comparative analysis of protein alignment algorithms in parallel environment using CUDA |
| title_full |
Comparative analysis of protein alignment algorithms in parallel environment using CUDA |
| title_fullStr |
Comparative analysis of protein alignment algorithms in parallel environment using CUDA |
| title_full_unstemmed |
Comparative analysis of protein alignment algorithms in parallel environment using CUDA |
| title_sort |
comparative analysis of protein alignment algorithms in parallel environment using cuda |
| publisher |
BRAC University |
| publishDate |
2016 |
| url |
http://hdl.handle.net/10361/5405 |
| work_keys_str_mv |
AT fahimshadman comparativeanalysisofproteinalignmentalgorithmsinparallelenvironmentusingcuda AT princegulshanjubaed comparativeanalysisofproteinalignmentalgorithmsinparallelenvironmentusingcuda AT hossainshehabul comparativeanalysisofproteinalignmentalgorithmsinparallelenvironmentusingcuda |
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1814309089462714368 |