GPALIGNER: A FAST ALGORITHM FOR GLOBAL PAIRWISE ALIGNMENT OF DNA SEQUENCES

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HADIAN DEHKORDI MOSTAFA; MASOUDI NEJAD ALI; MOHAMAD MOURI MORTEZA

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Journal Paper

Paper Information

Journal: Iranian Journal of Chemistry and Chemical Engineering Year:2011 | Volume:30 | Issue:2 (58) Page(s): 139-146

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Title

GPALIGNER: A FAST ALGORITHM FOR GLOBAL PAIRWISE ALIGNMENT OF DNA SEQUENCES

Author(s)

HADIAN DEHKORDI MOSTAFA | MASOUDI NEJAD ALI | MOHAMAD MOURI MORTEZA | Issue Writer Certificate

Keywords

SEQUENCE ALIGNMENT

PAIRWAISE ALIGNMENT

SEQUENCE COMPARISON

DYNAMIC PROGRAMMING

SPACED SEEDS

Abstract

Bioinformatics, through the sequencing of the full genomes for many species, is increasingly relying on efficient global alignment tools exhibiting both high sensitivity and specificity. Many computational algorithms have been applied for solving the SEQUENCE ALIGNMENT problem. DYNAMIC PROGRAMMING, statistical methods, approximation and heuristic algorithms are the most common methods applied to this problem. We introduce gpALIGNER, a fast pairwise DNA-DNA global alignment algorithm. gpALIGNER uses similar score schema with DIALIGN-T to produce the final alignment. It also uses the concept of "spaced seeds" to determine locally aligned subsequences which construct semi-global alignment as the preliminaries of global alignment computation. This enables gpALIGNER to have the precision provided by the DIALIGN-T algorithm in considerably less time and space complexities. We performed benchmarking of our approach based on numerous datasets from standard benchmarking databases and real sequences of NCBI database where gpALIGNER performed three times faster than DIALIGN-T. gpALIGNER is a new alternative for having sensitivity and selectivity of DIALIGN-T but with less computational cost.

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APA: Copy

HADIAN DEHKORDI, MOSTAFA, MASOUDI NEJAD, ALI, & MOHAMAD MOURI, MORTEZA. (2011). GPALIGNER: A FAST ALGORITHM FOR GLOBAL PAIRWISE ALIGNMENT OF DNA SEQUENCES. IRANIAN JOURNAL OF CHEMISTRY AND CHEMICAL ENGINEERING (IJCCE), 30(2 (58)), 139-146. SID. https://sid.ir/paper/585036/en

Vancouver: Copy

HADIAN DEHKORDI MOSTAFA, MASOUDI NEJAD ALI, MOHAMAD MOURI MORTEZA. GPALIGNER: A FAST ALGORITHM FOR GLOBAL PAIRWISE ALIGNMENT OF DNA SEQUENCES. IRANIAN JOURNAL OF CHEMISTRY AND CHEMICAL ENGINEERING (IJCCE)[Internet]. 2011;30(2 (58)):139-146. Available from: https://sid.ir/paper/585036/en

IEEE: Copy

MOSTAFA HADIAN DEHKORDI, ALI MASOUDI NEJAD, and MORTEZA MOHAMAD MOURI, “GPALIGNER: A FAST ALGORITHM FOR GLOBAL PAIRWISE ALIGNMENT OF DNA SEQUENCES,” IRANIAN JOURNAL OF CHEMISTRY AND CHEMICAL ENGINEERING (IJCCE), vol. 30, no. 2 (58), pp. 139–146, 2011, [Online]. Available: https://sid.ir/paper/585036/en

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