2. EMBL
• INTRODUCTION: EMBL (EUROPEAN MOLECULAR BIOGICAL INFORMATION)
• THIS IS THE ONE OF THE WORLD’S LEADING RESEARCH INSTITUTIONS AND
EUROPE FLAGSHIP LABORATORY FOR THE LIFE SCIENCES.
• LOCATION-WELCOME TRUST GENOME CAMPUS IN HINXTONS,UK ALONG WITH
WELCOME TRUST SANGER INSTITUTE.
• FOUNDED IN -1974
• HISTORY-EMBL-NUCLEOTIDE SEQUENCE DATE LIBRARY.
• EMBL COUNCIL VOTED FOR ESTABLISHING EBI.
3. CLUSTALW
• THIS IS THE THIRD GENERATION, RELEASED IN 1994.
• THIS IS PRODUCED BY JULIE D ,THOMSON ,TOBY AND GIBSON OF EUROPEAN
MOLECULAR BIOLOGY LABORATORY GERMANY AND DESMAND HIGGINS OF
EUROPEAN BIOINFORMATICS INSTITUTE CAMBRIDGE, UK AND AGROTHMICS.
• THIS IS AN BASIC MULTIPLE ALIGNMENT PROGRAM THAT USES SEEDED GUIDE
TREES AND HMM PROFILE-PROFILE
4. AIMS AND SCOPES
• EMBL-EBI MAINTAINS A COMPREHENSIVE RANGE OF AVAILABLE AND UP TO
DATE DATABASES WHICH COLLECTIVELY COVER THE FULL RANGE OF
MOLECULAR BIOLOGY, FROM NUCLEOTIDE SEQUENCE TO FULL SYSTEM.
• IT HAS A MANDATE TO MAKE IT’S TASK AND INFRASTRUCTURE FREELY
AVAILABLE TO THE GLOBAL SCIENTIFIC COMMUNITY.
• EMBL-EBI IS A CENTRAL PARTNER IN GLOBAL EFFORTS TO EXCHANGE
INFORMATION,SET STANDARDS, DEVELOP NEW METHODS AND CUARATE
COMPLEX INFORMATION.
5. TIME COMPLEXITY
• CLUSTALW HAS A TIME COMPLEXITY OF O(N2) BECOME OF IT’S USE OF THE
NEIGHBOURS JOINING METHOD.
• IT SAVES THE SIGNIFICANT AMOUNT OF TIME.
• IT TAKES ONE HOUR.
6. HOW WE CAN WORK ON CLUSTALW ON
LAPTOP OR MOBILE: ANALYZE OF DATA
• FIRST WE WILL GO ON NCBI WEBSITE.
• WE ASSUME THAT WE HAVE A PQQC GENE.
• THEN HERE WE SELECT THE ALL DATABASE OPTIONS AND SELECT THE NUCLEOTIDE OPTIONS IN THIS
.
• THEN,WE WRITE THE PQQC GENE IN SEARCH BAR.
• AFTER THAT ,WE WILL SEE THE LIST OF PQQC GENE AND SELECT ONE OF THEM.
• AFTER SELECT THE GENE ,WE CLICK ON PARTICULAR GENE AND GET A SEQUENCE OF THAT
PARTICULAR GENE.THEN ,WE GO ON FASTA FORMAT AND GET A SEQUENCE OF THAT PARTICULAR
GENE NUCLEOTIDE ON FASTA FORMAT.
• THEN WE COPY THIS FAST SEQUENCES AND GO ON BLAST WEBSITE AND HERE,WE SELECT
NUCLEOTIDE BLAST AND IN IT ,WE COPY THE FASTA SEQUENCE.
7. CONTINUOUS....
• RUN THE BLAST NUCLEOTIDE.
• WE GET MANY DOWNLOADED FILES IN BLAST FORMAT (FASTA ALIGNED).
• SELECTION GENE SEQUENCES AND DOWNLOAD.
• THEN COPY THE DOWNLOAD.
• THEN WE WILL GO ON WWW.GENOME.JP(MULTIPLE SEQUENCE ALIGNMENT CLUSTALW).
• HERE WE WILL SEE A BOX.
• PASTE THE SEQUENCE FROM BLAST IN IT.
• THEN EXECUTE MULTIPLE SEQUENCE ALIGNMENT.
• RESULTS IS READY.AFTER THIS WE CAN MAKE PHYLOGENETIC ANALYSIS.
• ALL THIS PROCESS IS GIVEN AS A FIGURE IN NEXT SLIDES.
20. ACCURACY AND RESULTS
• ALGORITHM CLUSTALW USES PROVIDES A CLOSE TO OPTIMAL RESULTS ALMOST
EVERY TIME.
• HOWEVER , IT DOES EXCEPTIONALY WELL WHEN THE DATA SET CONTAINS
SEQUENCES WITH VARIED DEGREE OF DIVERGENCE.
• THIS IS BECAUSE IN DATA SET LIKE, THIS IS THE GUIDE TREE BECOMES LESS SENSITIVE
TO NOISE.
• BUT THERE IS A LEAST LOSE OF ACCURACY THAT OTHER SOFTWARE DOESN’T HAVE
DUE TO THIS.
• WHEN THIS TESTED AGAINST MAFFT,T-COFFEE,CLUSTAL OMEGA AND OTHER MSA,IT
HAD LOWEST ACCURACY.
• IT HAD THE LEAST RAM MEMORY.
21. APPLICATION
• 1.USED FOR ALIGNING MULTIPLE NUCLEOTIDE PROTEIN SEQUENCE IN AN
EFFICIENT MANNER.
• 2.WE CAN USE IN MANUAL PRIMER DESIGNING WITH CLUSTALW.
• 3.THEY ARE MANY VERSION OF THE CLUSTAL OVER THE DEVELOPMENT OF THE
ALGORITHM ARE USED IN PRESENT TIME TO DO MULTIPLE SEQUENCE
ALIGNMENT.
