Mr.Kulachat Sae - Jang

Ph.D student in Medical Technology

4436692 MTMT/D

Group 17

Assignment two

Questions & Answers

Principle of nucleic acid analysis

By Dr. Kriengkrai Porkaew

Question : What is different between Global and Local alignment?

Answer : Global alignment tries to find the best alignment between two sequences. The global alignment align the whole sequences. Local alignment tried to find the best alignment between any subsequence from one sequence and any subsequence from another sequence.

Question : Can the two methods of alignment use blast for help our?

Answer : BLAST stands for Basic Local Alignment Search Tool. It is for local alignment.

More info on BLAST at www .ncbi.nlm.nih.gov/Blast

Question : What is the gap penalty?

Answer : Gap penalty is a way to penalize an alignment that introduces a gap. When you align two things, say - abcdef and abef, you would prefer to align like this: ABCDEF AB- -EF so that ab and ef of both sequences match. That would open a gap. The gap penalty will reduce the degree of match. > 4.How add gap penalty in base sequence? I don't quite understand the question. Partly, this question is answered in the previous question.

Grid computing, Parallel computing and bioinformatics development

By Dr. Sissades Tongsima

Question : What is the conception meaning and principle of Grid and Parallel Computing?

Answer : Parallel computing is the concept adopted by various fields to improve their applications' performance. It involves breaking up a job into some independent sub-jobs so that these jobs can be assigned to a group of workers (or processors) to execute them ***concurrently***. By doing so the sub-jobs which are much smaller than the original one can be completed in a short amount of time. Doing them in parallel (concurrent) allows finishing the subjobs at the same time resulting in improving the system performance. For Grid's definition, I would say that it has the parallel computing concept in it. However, it encompasses other important concepts such as "information sharing, resource sharing, promoting collaboration etc". I'd like you to look at it as the power grid concept where transmission lines and power plants are analogous to the internet and computing resources, respectively, in the Grid. The power produced by the power grid can be used by us whenever we connect our appliances' plugs to outlets. Very much the same way, the Grid wants to see the promotion of resources whenever users tap in to the internet. Since there are so many resources out there, the parallel processing concept is adopted to increase the overall computing performance such as the internet computing applications, seti@home and fightaids@home etc.

Question : What are the differentiation between Grid, Parallel Computing and General computer system?

Answer : From the above definition, you should now realize that the Grid concept is built upon the existing technologies. It makes uses of many general purpose systems which sometimes can have multiple processors in an individual system. The system that has multiple processors can be called parallel computer. The parallel computers can perform the underlying "parallel computation".

Question : Do you think that have development in Grid and Parallel Technology in the future? and Why? I

Answer : certainly do!! We are doing it right now. We hope that many people would benefit from the parallel computing and resource sharing in the Grid. Reason????.... hmmmm... well... imagining that you can now do research that requires some high performance computing resource(s) but you or your organization don't have the money to buy the system, using the grid would allow you to conduct your research uninteruptedly. You can also use some expensive equipment which you can not afford to have at your institution by accessing them via the grid service. The bottom line is "collaboration and sharing will be prosper with the Grid".

Please refer to www.globus.org for more information.

Knowledge Discovery in Databases

By Dr. Kitsana Waiyamai

Question : Could you please give me the example of Application in parallel computing in Thailand?

Answer : (I will update in this soon when Dr. Kitsana answer me)

Computational biology

By Dr. Chularat Tanprasert

Question : What are differentiation in concept meaning between Database and Datamining?

Answer : Database is a concept to define & store & manipulate set of related data. And the data mining is a set of tools to undiscovered patterns from a huge database.

Question : Do you think that may have higher level of its technology in the future?

Answer : It has a high possibility to have more advanced technologies in both fields.