Farah Dahman Bioinformatics 301 MOBILE ELEMENTS EXISTENCE IN MYCOBACTERIOPHAGES.

Slides:

Advertisements

Similar presentations

Diversity generating reverse transcriptase Reverse transcriptase an enzyme.

Advertisements

Phage BruceB, cluster G Et2Brutus, cluster A2.

Introduction to Bioinformatics Tuesday, 12 March.

Genomics – The Language of DNA Honors Genetics 2006.

Lecture 7 Gene Structure and Transposable Elements Gene structure Gene families Repetitive DNA including transposons Organelle genomes Reading: Chapter.

Statistics in Bioinformatics May 2, 2002 Quiz-15 min Learning objectives-Understand equally likely outcomes, Counting techniques (Example, genetic code,

Isolate phage Prepare phage for testing *Create high titer lysate via flooding method. *Isolate phage DNA and replicate using PCR. *Send off isolated phage.

Predicting Genes in Mycobacteriophages December 8, In Silico Workshop Training D. Jacobs-Sera.

Genomics Chapter 18.

Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity Nicholas M. Luscombe and Janet M. Thornton JMB (2002)

Origins of recently gained introns in Caenorhabditis Avril Coghlan and Kenneth H. Wolfe Department of Genetics, Trinity College Dublin, Ireland.

ECE 501 Introduction to BME

BIO 402/502 Advanced Cell & Developmental Biology I Section IV: Dr. Berezney.

Computational biology seminar

Genomes and Genetic Architecture. Life on Earth.

Statistics in Bioinformatics May 12, 2005 Quiz 3-on May 12 Learning objectives-Understand equally likely outcomes, counting techniques (Example, genetic.

University of Oklahoma Genome Center4/14/12.

Comparison of Drosophila Genomes Li-Lun, Ho. D. melanogaster vs. D. yakuba D. yakuba genome is assembled in Apr, D. yakuba genome has 14 times higher.

Biotechnology. Comparative genomics also has been used to identify recently mobilized transposons in genetically diverse humans. For example, over 600.

Todd J. Treangen, Steven L. Salzberg

Eukaryotic Gene Expression The “More Complex” Genome.

Homework #2 is due now Bonus #1 is due 10/24. deogr[Xpter:Xqter],genes[1.00: ]

Clustered Repeats and Regulatory Sites Abdulrahman Alazemi, Shahroze Abbas, Liam Lewis, Donald Ta, Ann Vo.

Yersinia Palindromic Sequences Introduction to Bioinformatics 301 April 30th, 2015 Jordan Davis.

Transposon and Mechanisms of Transposition

GenomesGenomes Chapter 21 Genomes Sequencing of DNA Human Genome Project countries 20 research centers.

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

Identification of large-scale genomic rearrangements between closely related organisms Bob Mau 1,2, Aaron Darling 1,3, Fred Blattner 4,5, Nicole Perna.

Genomes & their evolution Ch 21.4,5. About 1.2% of the human genome is protein coding exons. In 9/2012, in papers in Nature, the ENCODE group has produced.

Search for CRISPRs in mycobacteriophages

Bioinformatics PhD. Course Summary (approximate) 1. Biological introduction 2. Comparison of short sequences (

Mysterious Sequence Repeats in Phage Genomes AKHIL GARG BNFO 301 APRIL 30, 2015.

The metagenomics sequencing service CD Genomics. Metagenomics: Metagenomics is the study of metagenomes, genetic material recovered directly from environmental.

Data Mining the Yeast Genome Expression and Sequence Data Alvis Brazma European Bioinformatics Institute.

Copyright © 2009 Pearson Education, Inc. Art and Photos in PowerPoint ® Concepts of Genetics Ninth Edition Klug, Cummings, Spencer, Palladino Chapter 22.

Lecture 10 Genes, genomes and chromosomes

Analysis and comparison of very large metagenomes with fast clustering and functional annotation Weizhong Li, BMC Bioinformatics 2009 Present by Chuan-Yih.

.1Sources of DNA and Sequencing Methods.1Sources of DNA and Sequencing Methods 2 Genome Assembly Strategy and Characterization 2 Genome Assembly.

Define each of these terms: Chromosome: Gene: Allele: Genome: Mutation:

Chapter 21 Genomes and Their Evolution. Genomics ______________ is a new approach to biology concerned with the study of the ___________ set of __________.

Tracking Evolutionary Genetic Events in Group A Streptococcus Using Whole Genome Mapping J. Coppens 1, J. Sabirova 1, C. Lammens 1, K. Loens 2, S. Malhotra-Kumar.

It will help in preparing for the exam to read:

1 Microbial genetics (Ch. 7) Part 3 -- Creating genetic diversity Types of mutations Mutagens Transduction Conjugation Transformation Transposons.

 DNA- genetic material of eukaryotes.  Are highly variable in size and complexity.  About 3.3 billion bp in humans.  Complexity- due to non coding.

Lecture 2 Topic 1.

Cluster frequency for Phams found in Tortellini Genes 30-73

BrGSP: the Brassica 'A' genome sequencing project

Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite.

Genomes and Their Evolution

Genomes and their evolution

Allan J. Somers, Elizabeth Rutledge PhD., Salish Kootenai College

Bioinformatics tools to identify structured motifs in the upstream regions of stress-response-involved genes in Tetrahymena thermophila Antonietta La Terza*,

(B.P :51) ( B:P52 ).

Evolution of eukaryote genomes

attP region and attB regions

Fig Figure 21.1 What genomic information makes a human or chimpanzee?

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

مديريت موثر جلسات Running a Meeting that Works

Extra chromosomal Agents Transposable elements

Volume 32, Issue 6, Pages (March 2015)

Transposable Elements

Evolution of Genomes Chapter 21.

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

.1Sources of DNA and Sequencing Methods 2 Genome Assembly Strategy and Characterization 3 Gene Prediction and Annotation 4 Genome Structure 5 Genome.

GOMASHI ANNOTATION GENES 1-13

Organization of TCAST elements within T

SEQUENCE Start Initial situation Step 1 Step 2 Step 3 End

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

Presentation transcript:

Farah Dahman Bioinformatics 301 MOBILE ELEMENTS EXISTENCE IN MYCOBACTERIOPHAGES

Evolution of mycobacteriophage (transposons) (mosaicism) Mobile Elements MPEME1 & MPME2 BACKGROUND INFORMATION

Phages studied: Cluster F (average length- 57,422bp)  Fruit Loop, DotProduct, Bobi, Yoshi, Taj METHOD  

METHOD CONTINUED Run this method for each phage -compared sequence relations -repetitive sequence within each? -Mobile Element possibility

Classified their phages to have mobile element in them 5′-TTATC[a/t]GGGGT-3’ MPEME1 MPEME2 changes at positon 8 If find in phages, find match HOW TO KNOW IF MOBILE ELEMENT FOUND “Mycobacteriophages BPs, Angel and Halo: comparative genomics reveals a novel class of ultra-small mobile genetic elements.”

Results still being compared CONCLUSION