Biological sequence alignment on the computational grid using the GrADS framework

YarKhan, Asim; Dongarra, Jack

doi:10.1016/j.future.2005.02.002

Cited by 20 publications

(9 citation statements)

References 30 publications

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“…Parallelization of FASTA has been implemented in the Grid Application Development Software (GrADS) project [18]. The GrADS adapts the master-worker paradigm, scheduling and rescheduling the tasks on an appropriate set of resources, launching and monitoring the execution.…”

Section: A Related Workmentioning

confidence: 99%

Parallel Guided Dynamic Programming Approach for DNA Sequence Similarity Search

Nordin¹,

Yazid²,

Aziz³

et al. 2009

IJCEE

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 Development of DNA sequence comparison technique is an active research activity in computational biology application.Commonly techniques studied are dynamic programming and heuristic algorithms. Exhaustive dynamic programming algorithm produces optimal result but requires longer time and bigger space. Heuristic algorithm gives approximate results with much faster processing. We have developed a new model that improves the speed of large scale DNA sequence similarity search and at the same time the best possible alignment result is retained. The model is known as a guided dynamic programming approach for DNA sequence similarity search (FRA-Search). Two approaches are used to complete the FRA-Search model: an automaton based exact string matching algorithm is employed to skip irrelevant database sequences from being computed for dynamic programming alignment processing and; the rough sets theory has been employed to classify and reduct the dataset. This paper discusses the parallel model for FRA-Search application. The parallel FRA-Search model is implemented on PC-based cluster system. It is developed on a single program multiple data (SPMD) architecture and MPJ Express software is used as a communication interface protocol between processors.

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Section: A Related Workmentioning

confidence: 99%

Parallel Guided Dynamic Programming Approach for DNA Sequence Similarity Search

Nordin¹,

Yazid²,

Aziz³

et al. 2009

IJCEE

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“…Parallelization of FASTA has been implemented in the Grid Application Development Software (GrADS) project as in [11]. The GrADS adapts the master-worker paradigm, scheduling and rescheduling the tasks on an appropriate set of resources, launching and monitoring the execution.…”

Section: B) Agentmentioning

confidence: 99%

Designing and Building a Framework for DNA Sequence Alignment Using Grid Computing

Orabi¹,

Assal²,

Azim³

et al. 2014

ijacsa

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Abstract-Deoxyribonucleic acid (DNA) is a molecule that encodes unique genetic instructions used in the development and functioning of all known living organisms and many viruses. This Genetic information is encoded as a sequence of nucleotides (adenine, cytosine, guanine, and thymine) recorded using the letters A, C, G, and T.DNA querying or alignment of these sequences required dynamic programming tools and very complex matrices and some heuristic methods like FASTA and BLAST that use massive force of processing and highly time consuming. We present a parallel solution to reduce the processing time. Smith waterman algorithm, NeedlemanWunsch, some weighting matrices and a grid of computers are used to find field of similarity between these sequences in large DNA datasets. This grid consists of master computer and unlimited number of agents. The master computer is the user interface for insert the queried sequence and coordinates the processing between the grid agents.

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“…The BLASTP, FASTA and SW methods were successfully parallelized and Grid-enabled (e.g. [31][32][33]). …”

Section: Virtual Protein Sequence Databasesmentioning

confidence: 99%

The configuration space of homologous proteins: A theoretical and practical framework to reduce the diversity of the protein sequence space after massive all-by-all sequence comparisons

Bastien

Ortet

Roy

et al. 2007

Future Generation Computer Systems

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Biological sequence alignment on the computational grid using the GrADS framework

Cited by 20 publications

References 30 publications

Parallel Guided Dynamic Programming Approach for DNA Sequence Similarity Search

Parallel Guided Dynamic Programming Approach for DNA Sequence Similarity Search

Designing and Building a Framework for DNA Sequence Alignment Using Grid Computing

The configuration space of homologous proteins: A theoretical and practical framework to reduce the diversity of the protein sequence space after massive all-by-all sequence comparisons

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