PARALLEL SEARCHING ALGORITHM FOR SEQUENCES IN A DATABASE USING GRAPHICS PROCESSING UNIT

Q: How can I download an article?

To download an article from SID, first log in to the site, search for the article title, and click on the 'Download Article' option.

Q: How can I download an ISI article?

To download an ISI article on SID, enter the keyword or article title in the search bar, view the relevant results, click on the desired article, and select the 'Download Article' option.

Q: How can I access the SID database?

To access the SID database, visit SID.ir, create an account, and log in to access scientific resources.

Q: Is downloading articles from SID free?

Some articles on SID are available for free, while others require payment. Details are specified on the article's page.

NOURMOFIDI V.; PARSAEI M.; MADADKAR SOBHANI A.

Scientific Information Database (SID) - Trusted Source for Research and Academic Resources

Journal Paper

Paper Information

Journal: JOURNAL OF SCIENCE (UNIVERSITY OF TEHRAN) (JSUT) Year:2008 | Volume:34 | Issue:3 Page(s): 67-73

Download Full-Text

مرکز اطلاعات علمی Scientific Information Database (SID) - Trusted Source for Research and Academic Resources

Persian Verion

View:

1,893

Download:

Cites:

Information Journal Paper

Title

PARALLEL SEARCHING ALGORITHM FOR SEQUENCES IN A DATABASE USING GRAPHICS PROCESSING UNIT

Author(s)

NOURMOFIDI V. | PARSAEI M. | MADADKAR SOBHANI A. | Issue Writer Certificate

Keywords

SMITH-WATERMANQ3

SEQUENCE ALIGNMENTQ3

CUDAQ3

GPUQ3

Abstract

We present an algorithm for NVIDIA CUDA platform based on SMITH-WATERMAN algorithm for SEQUENCE ALIGNMENT problem. CUDA is a new programming language which is very similar to the standard C language, with some extensions. By using the SMITH-WATERMAN algorithm which is used to find similarity between two sequences by making a scoring matrix; this application tries to find the similarity between a sequence which called query sequence and sequences in a database file. In this program, each thread is used for calculating one scoring matrix between the query sequence and one of the sequences in database. The algorithm utilizes small but fast shared memory which is inside the GPU for holding four intermediate columns in each cycle for each thread. If the database is large enough, it can keep the GPU in full working order and results in better speedup in comparison to CPU. To demonstrate the performance, we used a high-end CPU, Intel Core 2 Due E6600 and a mid-end GPU, GeForce 8600GT and saw the speedup in about twenty times more than CPU.

Cites

No record.

References

No record.

Cite

APA: Copy

NOURMOFIDI, V., PARSAEI, M., & MADADKAR SOBHANI, A.. (2008). PARALLEL SEARCHING ALGORITHM FOR SEQUENCES IN A DATABASE USING GRAPHICS PROCESSING UNIT. JOURNAL OF SCIENCE (UNIVERSITY OF TEHRAN) (JSUT), 34(3), 67-73. SID. https://sid.ir/paper/2271/en

Vancouver: Copy

NOURMOFIDI V., PARSAEI M., MADADKAR SOBHANI A.. PARALLEL SEARCHING ALGORITHM FOR SEQUENCES IN A DATABASE USING GRAPHICS PROCESSING UNIT. JOURNAL OF SCIENCE (UNIVERSITY OF TEHRAN) (JSUT)[Internet]. 2008;34(3):67-73. Available from: https://sid.ir/paper/2271/en

IEEE: Copy

V. NOURMOFIDI, M. PARSAEI, and A. MADADKAR SOBHANI, “PARALLEL SEARCHING ALGORITHM FOR SEQUENCES IN A DATABASE USING GRAPHICS PROCESSING UNIT,” JOURNAL OF SCIENCE (UNIVERSITY OF TEHRAN) (JSUT), vol. 34, no. 3, pp. 67–73, 2008, [Online]. Available: https://sid.ir/paper/2271/en

Related Journal Papers