WMU CS 6260 Parallel Computations II

Spring 2013

Presentation #1 about Semester Project

Feb/18/2013

Professor: Dr. de Doncker

Name: Sandino VargasXuanyu Hu

Implementation and Analysis of Parallel

Motif Finding Algorithms for Bioinformatics

Our Team of This Semester ProjectProject Topic Background: BioinformaticsParallel Algorithms in BioinformaticsProblem We Want to SolveSolution in a Sequential WayDemo of Sequential ProgramHow to Parallelize It? (paper)ConclusionReferenceQuestions?

Outline

Members of our team:Sandino VargasXuanyu Hu

We have taken the same coursesWMU_CS6030_Bioinformatics (Summer II

2012)WMU_CS5260_Parallel Computation IWMU_CS6260_Parallel Computation II (Spring

2013)Our professor, Dr. de Doncker, will be

teaching the interesting course CS6030 "Biomedical Informatics“ again, in the next semester: Summer I (2013).

Our team of Semester Project

Bioinformatics is an interdisciplinary field that develops and improves upon methods for storing, retrieving, organizing and analyzing biological data.

A major activity in bioinformatics is to develop software tools to generate useful biological knowledge.

Project Topic Background: Bioinformatics

Mapping DNASequencing DNAComparing SequencesPredicting GenesFinding SignalsIdentifying ProteinsRepeat AnalysisDNA ArraysGenome RearrangementsMolecular Evolution

Subjects in Bioinformatics

After we read the materials and searched the internet, we both agreed that Sequencing DNA is the best object for implementation and analysis of parallel computations.

There will be 3 major questions:What is Sequencing DNA?Why we need Sequencing DNA?How to Sequencing DNA?

Sequencing DNA

DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule. It includes any method or technology that is used to determine the order of the four bases—adenine, guanine, cytosine, and thymine—in a strand of DNA.

The advent of rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery.

What is Sequencing DNA?

This is a picture of a DNA model2 strands and made of 4 kinds of pairsA-T != T-A

A – TT – AG – CC – G

One Thing We Need to Know

DNA sequencing may be used to determine the sequence of individual genes, larger genetic regions, full chromosomes or entire genomes.

Depending on the methods used, sequencing may provide the order of nucleotides in DNA or RNA isolated from cells of animals, plants, bacteria, or any other source of genetic information.

Why we need Sequencing DNA?

The resulting sequences may be used by researchers in molecular biology or genetics to further scientific progress or may be used by medical personnel to make treatment decisions or aid in genetic counseling.

Function = DNA PatternDNA Function:

Estimate the function of a new kind of virusKill the virus’s function by starvation

Why we need Sequencing DNA?

In genetics, a mutation is a change of the nucleotide sequence of the genome of an organism, virus, or extra-chromosomal genetic element.  

Mutations may or may not produce changes in the observable characteristics of an organism.

Mutations play a part in both normal and abnormal biological processes, including evolution, cancer, and the development of the immune system.

Another Thing We Need to Know

Gene Mutation

Lots of methods:Maxam-Gilbert sequencingChain-termination methodsShotgun sequencingBridge PCRPolony sequencing454 PyrosequencingIon semiconductor sequencingDNA nanoball sequencing

How to Sequencing DNA?

Parallel Computing in Bioinformatics

Web Site URL: http://www.gpugrid.net/

We have several DNA strands, and some of them might have mutation.

They have the same function. Or they are from the same species.

We want to find the DNA pattern that make them to have the same function.

DNA is made of 2 strands, each stain is made of A, T, G, C. If we know one of the 2 stains, we can easily know another one.

Problem We Want to Solve

ExamplesATGCAACT is the DNA

pattern we want to find.Small letter means

mutation.

Greedy Algorithm

Solution in a Sequential Way

Brute Force

Solution in a Sequential Way

Branch And Bound:

Solution in a Sequential Way

Demo of Sequential Program

Some materials about my semester projectBioinformaticsSequencing DNAParallel Algorithms in BioinformaticsProblem We Want to SolveSolution in a Sequential WayHow to Parallelize It (paper)

Conclusion

I would be very happy to answer any questions you have.

Questions?

Thank You

http://en.wikipedia.org/wiki/Bioinformaticshttp://en.wikipedia.org/wiki/DNA_sequencinghttp://www.gpugrid.net/http://meseec.ce.rit.edu/756-projects/spring2006/

d2/1/Bioinformatics.pdfhttp://www.ac.uma.es/~ots/papers/survey.pdfhttp://eprints.ru.ac.za/162/1/Akhurst_MSc.pdfhttp://en.wikipedia.org/wiki/Mutationhttp://

www.cs.washington.edu/education/courses/cse527/04au/proj/lyons-talk.pdf

http://www.cs.washington.edu/education/courses/cse527/04au/proj/lyons-paper.pdf

Reference