Reports on attending workshop on Genomic and Bioinfomatic

(for all medical application)

Date:           8 July 2008

Time:           2:00-5:00p.m.

Venue:         Computer lab of SMJK Yu Hua, Kajang

Organizer: Malaysia Genomic Research Centre (MGRC)

Speakers:  Ezzeddin Kamil bin Mohd Hashim, Amy Chin, Noraisyah, Mazlina,  

                  Yong Shuih Rong and project manager.

Participants: Students of 6BS2 and 6BS3 leaded by Puan Sang Fay Lee and

                     Puan Noraini Mohammad Ali

Flow Of the workshop

·        Registration

v    Register to get free booklet on the course and certificates will be given later.

·        Welcome speech

v     Puan Sang introduced all the lecturer from MGRC, they are :  Ezzeddin Kamil bin Mohd Hashim, Amy Chin, Noraisyah, Mazlina, and Yong Shuih Rong.

v     Puan Sang represented principal to give his speech,she also said that this is a good chance for the students to explore more about Genomic and Bioinformatic.

v     She invited the Master of the ceremony, Cik Mazlina to take over the ceremony.

v     Cik Mazlina briefed the students about the Genomic.

·        Mr Ezzeddin Kamil bin Mohd Hashim with his Fundamentals of Genomic and Bioinformatics.

v     Nucleic acid and the amino acid

Ø     All genetic information in any living creature is stored in deoxyribonucleic acid(DNA) and ribonucleic acid(RNA)

Ø     DNA is made up of Adenine(A), Guanine(G), Cytosine(C) and Thymine(T).

Ø     RNA is made up of Adenine(A), Guanine(G), Cytosine(C) and Uracil(U).

Ø     Nucleic acid forms a double helix, which comprise two spiral-shape strand and polypeptides running in opposite directions.

Ø     All protein are made up of blocks of amino acids which consists of a central carbon atom(C), an anime group NH2, a carboxyl group(COOH) and a variable chain R.

v     Transcription, Translation and Protein Synthesis

Ø     Transcription is the process of transforming genetic information from DNA to RNA. There are 3 stages of transcription, namely ignition, elongation and termination.

Ø     Translation is the process that sythesis protein based on the messenger RNA(mRNA), transfer RNA(tRNA), and ribosomal RNA(rRNa) and Guanosine-5’-triphospahte(GTP)

v     Gene Regulation

Ø     Is a cellular process that controls the production of functional cellular components.

Ø     This provide the basic for cellular differentiation, morphogenesis, versality and adaptability of the cell and organism.

Ø     Gene regulation in eukaryotes is more complicated than in prokaryotes.

v     Genome Evolution & Mutation

Ø     Evolution

ü      Changes in the heritable traits of an individual in a population from one generation to the next.

ü      Changes in traits or inheritable genes can be due to transfer of gene between populations, between species and other possible modes gene of transfer.

Ø     Mutation

ü      Base pairs level analysis has shown that the difference can be induced by various mutagens.

ü      There are 2types of gene mutation, Germ line mutation and somatic mutation.

v     Common Underlying Principles in All Application

Ø     In bioinformatics, the most used of sequence analysis is sequence alignment

Ø     It is method of arranging the primary sequences of DNA, RNA or protein to identify regions of similarity.

Ø      FASTA is the most common sequence format encountered in the sequence analysis.

Ø      A FASTA file may contain more than one sequence.

Ø     A general global alignment technique which is mainly used is the Needleman-Wunsch algorithm and it is based on dynamic programming.

·        Noraisyah sharing her research with the students.

v    She had made a research on platypus.

v    She found that platypus are very special animals due to their sex chromosome.

v    The platypus will change their gender according to the surrounding temperature which is rarely seen in other animals.

BREAK FROM 3:15pm TO 3:45pm

·        Amy Chin with her talk on “SYNA-“

v    Amy Chin taught the students about the usage of the syna- icon whih appeared at the front page of their web page. (http://www.mgrc.com.my/)

v    There are 6 syna- application which are :-

                                                     I.      Synablast

ü     Is a sequence similarity search sequences stored in synaBASE

ü     Has the “look and feel” of NCBI BLAST.

                                                II.      Synasearch

ü     Is a web-based sequence alignment and searching tool specifically designed to interrogate pattern information in synaBASE.

ü     Is similar to NCBI-BLAST

ü     Users familiar with tools such as NCBI BLAST and FASTA are able to use synaSEARCH for the same purpose as these programs

                                           III.      Synatate

ü     Is designed to identify structural and functional motifs in query sequences using the presictability of synaBASE pattern.

                                               IV.      Synacompare

ü     Is a comparative genomics application used to analyse single and multiple sequences from genomes to those stored in synaBASE.

ü     There are 3 methods to submit sequences.

                                                    V.      Synaprobe

ü     Is a tool used to design probe for gene or mRNA transcripts

ü     Enable the users to find the best probe sequences by weighting the following parameters according to user defined input settings.

                                               VI.      Synahybridies

ü      Is a web-based application for finding potential binding sites of microarray probe

ü      It is based on the synaBASE API method SXSSASearch.

·        The ending of the ceremony.

v    The workshop end about 5:30pm with Puan Sang presenting souvenirs to MGRC staffs.

v    Everyone was very happy because we gained a lot of knowledge during the workshop.

v    I would like to represent all my fellow friends to thanks the speakers from MGRC and our teachers, Puan Sang and Puan Noraini Mohammad Ali.