Enabling Multiple Sequence Comparison by Log- Expectation (MUSCLE) on EUAsiaGrid EUAsiaGrid Master Class 6 May 2010 By: Lee Hong Kai and Thomas Tay NUHS.

Slides:

Advertisements

Similar presentations

April 15, 2010 Marcy McMillian Effie Boothe

Advertisements

Virus Classification And Description. Classification Parameters Several Parameters Are Used for Classification –Viral classification study is referred.

Human rhinovirus species occurrence among adults with respiratory tract infection and asymptomatic individuals during two consecutive winter seasons Zlateva.

Overview of Molecular Epidemiological Methods for the Subtyping and Comparison of Viruses Derek Wong

Current methods for high-throughput resequencing of custom targets Adam Gordon Nickerson Lab, UW Genome Sciences WHI Genetics SIG call 3/26/14.

Search for cellular attachment receptors used by a GII.4 Norovirus Dijon Gaurav Dutta Dwivedi Supervisors: Niklas Arnberg and Carin Årdahl.

Epidemiology J Endemic, epidemic or pandemic? Disease prevention

DNA Technologies – Southern Blotting & ELISA By C. Kohn, Waterford WI.

Sapovirus Outbreaks in Long-Term Care Facilities

Noroviruses an emerging infection

1 Single Nucleotide Polymorphisms (SNP) Gary Jones SPE, Technology Center 1600 (703)

Next-generation sequencing

Genomics, Cancers & Infectious Diseases Qunyuan Zhang Division of Statistical Genomics Washington University School of Medicine.

BIOINFORMATICS Ency Lee.

An analysis of “Bioinformatics analysis of SARS coronavirus genome polymorphism” by Pavlović-Lažetić, et. al Angela Brooks July 9, 2004 SoCalBSI Article.

Molecular Diagnosis of Infectious Diseases. Why use a molecular test to diagnose an infectious disease? Need an accurate and timely diagnosis Important.

HIV/AIDS as a Microcosm for the Study of Evolution.

Informatics Support for Vaccine Projects Using and extending the UCSC bioinformatics infrastructure.

New Molecular Based Methods of Diagnosis

Norwalk Virus Scott VasporyCraig Pritch October 4, 2005.

The Central Dogma of Molecular Biology (Things are not really this simple) Genetic information is stored in our DNA (~ 3 billion bp) The DNA of a.

Virus Evolution Molecular Epidemiology of Viral Infections Jen-Ren Wang, Ph. D. 王貞仁 Dept. of Medical Laboratory Science and Biotechnology National Cheng.

Gastro Enteritis Outbreak in A Residential Complex for the Elderly ? First Case Peak State/Local dept. Involved Prelim Norvo CDC 23 rd 24 th 29 th

Detection of parvovirus B19 and novel human parvoviruses in high-risk individuals Ashleigh Manning 1, Kate Templeton 2, Ed. Gomperts 3, Peter Simmonds.

Laboratory Training for Field Epidemiologists Typing May 2007 Sequencing and Phylogeny.

The evolution of infectious disease. Influenza We generally think of the flu as nothing more than a minor annoyance In an average year, however, the flu.

Materials and Methods Stool Collection Six stool specimens from patients who had contracted gastroenteritis were collected from the Coronary Care Unit.

Lee H. Harrison, MD Associate Professor

InCoB August 30, HKUST “Speedup Bioinformatics Applications on Multicore- based Processor using Vectorizing & Multithreading Strategies” King.

Molecular Techniques in Microbiology These include 9 techniques (1) Standard polymerase chain reaction Kary Mullis invented the PCR in 1983 (USA)Kary.

Development and Application of SNP markers in Genome of shrimp (Fenneropenaeus chinensis) Jianyong Zhang Marine Biology.

Grid enabling phylogenetic inference on virus sequences using BEAST - a possibility? EUAsiaGrid Workshop 4-6 May 2010 Chanditha Hapuarachchi Environmental.

REASSORTMENT OF INFLUENZA VIRUS

MUSCLE An Attractive MSA Application. Overview Some background on the MUSCLE software. The innovations and improvements of MUSCLE. The MUSCLE algorithm.

Molecular biology and evolution in genomics era Li Jun and Frederick C.C. Leung 5N01, School of Biological Science, The University.

Influenza H1N1 A: A close insight Dr. Mustafa Ababneh Molecular Virologist.

Masters Programme in Genomic Medicine Open Day Event Tendering process Anne Gilford, Head of Education and Quality, HEWM 3 rd September.

The New Influenza A/H1N1 Isabelle Thomas May 28-29, 2009 Brussels,

Viral Genomics: Strength in Numbers David Spiro Assistant Investigator J. Craig Venter Institute

Overview: Molecular Epi

Nada M. Melhem, PhD American University of Beirut

FAMILY CALICIVIRIDAE. Viral Morphology Non-enveloped: nm (+) ss RNA Some cultivable and some no Replication: cytoplasm.

Other uses of DNA microarrays

NCBI: something old, something new. What is NCBI? Create automated systems for knowledge about molecular biology, biochemistry, and genetics. Perform.

Work Presentation Novel RNA genes in A. thaliana Gaurav Moghe Oct, 2008-Nov, 2008.

I Introduction to influenza Department of Health 2016 Vaccination Campaign Training workshop Presentation developed by the National Institute for Communicable.

Supplementary Fig. 1 ClustalW (2.1) multiple sequence alignment and comparison of deduced partial protein sequences of SOS1 in root tissues of wheat genotypes.

© 2004 Wadsworth – Thomson Learning Chapter 20 Preventing Disease.

Session 3: Molecular Epidemiology Introduction

Computing challenges in working with genomics-scale data

Evolution of rubella viruses following long term endemic circulation

Infectious Diseases Surveillance in the Military

Use of next generation Sequencing (NGS) at a National Reference Laboratory, Denmark 2015/16 Authors: Thea Kølsen Fischer, Ramona Trebbien, Jannik Fonager,

Molecular epidemics of Norovirus related Outbreak in Korea

Relationship between Genotype and Phenotype

Relationship between Genotype and Phenotype

Accurate genotyping of hepatitis C virus through nucleotide sequencing and identification of new HCV subtypes in China population Y.-Q. Tong, B. Liu,

Laboratory Diagnosis of Clostridium difficile Infection

Accurate genotyping of hepatitis C virus through nucleotide sequencing and identification of new HCV subtypes in China population Y.-Q. Tong, B. Liu,

A Web-based Interactive Genome Library for Surveillance, Detection, Characterization and Drug-Resistance Monitoring of Influenza Virus Infection in the.

Volume 381, Issue 9877, Pages (May 2013)

M.W. Borgdorff, D. van Soolingen Clinical Microbiology and Infection

Molecular diagnostic and genetic characterization of highly pathogenic viruses: application during Crimean–Congo haemorrhagic fever virus outbreaks in.

A. McNally, F. Alhashash, M. Collins, A. Alqasim, K. Paszckiewicz, V

Precomputing Edit-Distance Specificity of Short Oligonucleotides

Molecular epidemiology and genetic diversity of human astrovirus in South Korea from 2002 to 2007 A.Y. Jeong, H.S. Jeong, M.Y. Jo, S.Y. Jung, M.S. Lee,

Relationship between Genotype and Phenotype

Presentation transcript:

Enabling Multiple Sequence Comparison by Log- Expectation (MUSCLE) on EUAsiaGrid EUAsiaGrid Master Class 6 May 2010 By: Lee Hong Kai and Thomas Tay NUHS Molecular Diagnostic Center

Norovirus Main pathogen causing non-bacterial outbreaks of gastroenteritis Easily transmitted in semi-closed communities such as hospitals and long-term care facilities Extremely infectious and a potentially dangerous pathogen when present in immunocompromised patients.

Norovirus Small, round +ssRNA virus of about 50nm Genome size of about 7.5kb, encoding: - major structural protein, VP1 - minor caspid protein, VP2 Genetically and antigenically diverse –genotyping of virus strains to determine epidemiology link of infected patients in an epidemic outbreak or transmission event.

Purpose A need for multiple sequence alignment of norovirus from genogroup I, II and IV ‣ Effective primer probe design ‣ Phylogeny analysis (sequence editing) ‣ SNP analysis ‣ Check sequence variability

Problem ClustalW takes 9hrs for about 1000 sequences MUSCLE is much faster by still limited by memory MUSCLE v3.6 by Robert C. Edgar This software is donated to the public domain.Please cite: Edgar, R.C. Nucleic Acids Res 32(5), noro 6423 seqs, max length 7746, avg length :05:08 10 MB(2%) Iter % K-mer dist pass 1 00:05:10 10 MB(2%) Iter % K-mer dist pass 2 muscle(1066) malloc: *** mmap(size= ) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug *** OUT OF MEMORY *** Memory allocated so far 10 MB

Thank You!