ToxoDB ApiDB Workshop June 2006.

Slides:



Advertisements
Similar presentations
Sequencing a genome. Definition Determining the identity and order of nucleotides in the genetic material – usually DNA, sometimes RNA, of an organism.
Advertisements

Doug Brutlag 2011 Sequencing the Human Genome Doug Brutlag Professor Emeritus of Biochemistry.
Welcome to Introduction to Bioinformatics Wednesday, 10 February Genome Sequencing/Assembly Genome sequencing/Assembly Click anywhere to go on to the next.
WGS Assembly and Reads Clustering Zemin Ning Production Software Group Informatics Division.
SEQUENCING-related topics 1. chain-termination sequencing 2. the polymerase chain reaction (PCR) 3. cycle sequencing 4. large scale sequencing stefanie.hartmann.
DNA Sequencing – “Plus and Minus” Plus –Incubate with T4 DNA Polymerase and single dNTP –T4 Polymerase degrades 3’ ends in absence of dNTP –Fractionated.
Mining SNPs from EST Databases Picoult-Newberg et al. (1999)
Positional Cloning LOD Sib pairs Chromosome Region Association Study Genetics Genomics Physical Mapping/ Sequencing Candidate Gene Selection/ Polymorphism.
The Human Genome Race. Collins vs. Venter Collins Venter.
Sequencing Informatics Gabor T. Marth Department of Biology, Boston College BI420 – Introduction to Bioinformatics.
Expanding the Tool Kit for BAC Extension Summary of completion criteria developed for NSF Tomato Sequencing Workshop January 14, 2007.
Central Dogma Information storage in biological molecules DNA RNA Protein transcription translation replication.
Sequencing Informatics Gabor T. Marth Department of Biology, Boston College BI420 – Introduction to Bioinformatics.
CS273a Lecture 1, Autumn 10, Batzoglou DNA Sequencing.
Reminder: Class on Friday, Discussion of Li et al. Proposal/Projects CAMERA feedback?
Genome sequencing. Vocabulary Bac: Bacterial Artificial Chromosome: cloning vector for yeast Pac, cosmid, fosmid, plasmid: cloning vectors for E. coli.
Genome Assembly Bonnie Hurwitz Graduate student TMPL.
DNA Sequencing. Fig
William S. Klug Michael R. Cummings Charlotte A. Spencer Concepts of Genetics Eighth Edition Chapter 19 Recombinant DNA Technology Copyright © 2006 Pearson.
Genome closure and finishing. Clone walking Already sequenced Unsequenced primer locations tgcatgatcgtgatcat acgtactagcactagtactgtagtcgatgcactgatcgatcgatcgatgctacgatgcatgct...
Presentation on genome sequencing. Genome: the complete set of gene of an organism Genome annotation: the process by which the genes, control sequences.
Mouse Genome Sequencing
Chromosome 8 Sequencing: Current Status and Future Prospects toward Finishing Shusei Sato, Erika Asamizu, Takakazu Kaneko, Hiroyuki Fukuoka, Satoshi Tabata.
Kerstin Howe, Mario Caccamo, Ian Sealy The Zebrafish Genome Sequencing Project Bioinformatics resources.
Genome Sequencing and Assembly
Whole genome scans to localise QTL X. Likely positionQTL Chromosome with mapped markers BAC Contig Spanning QTL region New MarkersCandidate Genes Fine.
Biotechnology pp WHAT IS IT?  Biotechnology : the application of technology to better use DNA and biology.
Genome sequencing Haixu Tang School of Informatics.
Genome Sequencing in the Legumes Le et al Phylogeny Major sequencing efforts Minor sequencing efforts ~14 MY ~45 MY.
Steps in a genome sequencing project Funding and sequencing strategy source of funding identified / community drive development of sequencing strategy.
Sequencing a genome. Approximate Molecular Dynamics: New Algorithms with Applications in Protein Folding Author: Qun (Marc) Ma Predicting the 3D native.
Status report on gap closure of the human chromosome 5 BAC map Authentication of C5 BAC maps Map and sequence status Gap status and steps used to close.
Revision – Concept map.
The Changing Face of Sequencing
Stratton Nature 45: 719, 2009 Evolution of DNA sequencing technologies to present day DNA SEQUENCING & ASSEMBLY.
Human Genome.
What do we already know ? The rice disease resistance gene Pi-ta Genetically mapped to chromosome 12 Rybka et al. (1997). It has also been sequenced Bryan.
Microbial Genetics. DNA is the Genetic Material Griffiths Avery et al.
Mojavensis: Issues of Polymorphisms Chris Shaffer GEP 2009 Washington University.
Slide 1 of 24 Copyright Pearson Prentice Hall 12-4 Mutations 12–4 Mutations.
CISC667, S07, Lec4, Liao CISC 667 Intro to Bioinformatics (Spring 2007) Whole genome sequencing Mapping & Assembly.
Excellent cell biology hormone and light signaling pathways operative few cell types & simple developmental pattern polar tip growth and division tolerant.
Genome Analysis. This involves finding out the: order of the bases in the DNA location of genes parts of the DNA that controls the activity of the genes.
Molecular Basis for Relationship between Genotype and Phenotype DNA RNA protein genotype function organism phenotype DNA sequence amino acid sequence transcription.
Physical Map and Organization of Arabidopsis thaliana Chromosome 4
Microbial genomics.
BrGSP: the Brassica 'A' genome sequencing project
3. genome analysis.
Pre-genomic era: finding your own clones
Construction of clone-based physical maps suitable for sequencing the human genome. The first-generation physical maps of human chromosomes constructed.
Stephen W Scherer, Joseph Cheung  Current Biology 
BAC-Based Physical Map of the Rice Genome.
Genome sequencing informatics
Lecture 9 Genome Mapping By Ms. Shumaila Azam
CSCI 1810 Computational Molecular Biology 2018
Introduction to Sequencing
Sequence the 3 billion base pairs of human
A, genomic copy number profiles of chromosome 8 with array CGH in SUM-44, -52, and A, genomic copy number profiles of chromosome 8 with array CGH.
Mutation Notes.
Cell Transformation.
Relationship between Genotype and Phenotype
Linear schematic of the basic quality control procedure for marker gene (microbiome) data. Linear schematic of the basic quality control procedure for.
The genomic distribution of essential and non-essential mouse genes, separated into known and predicted essentiality. The genomic distribution of essential.
Fine mapping of SRT1. Fine mapping of SRT1. To fine map the SRT1 locus, we compared the sequencing data and developed a set of InDel markers in the 5 Mb.
Whole-chromosome view of gene density, inverse environmental variation, inverse total variation, and open chromatin signature. Whole-chromosome view of.
Comparative mapping of LG1 of the white grouper (center) and its syntenic LGs EBR13 of the kelp grouper (right), and ECO8 of the orange-spotted grouper.
Copyright Pearson Prentice Hall
Mapping of srt1 by BSA-seq.
THE HUMAN GENOME PROJECT. Gene Myers Let’s sequence the human genome with the shotgun strategy That is impossible, and a bad idea anyway Phil Green 1997.
Relative abundance and expression of the 10 most abundant MAGs in the bioreactor at day 96. Relative abundance and expression of the 10 most abundant MAGs.
Presentation transcript:

ToxoDB ApiDB Workshop June 2006

Shotgun Sequencing Strategy genetic markers C810-A6 SAG4 Bs328 sourceDNA end sequencing of small insert plasmid library end sequencing of larger insert libraries (BAC/cosmid/plasmid) assembly scaffold physical gap sequence gaps

Sequencing Scaffolds Pinned to the Genetic Map: chromosomes 1a & 1b (Sanger) whole genome shotgun (TIGR) unmapped markers (telomeric?) mapping ambiguities Sequencing & assembly: Ian Paulsen, Neil Hall Genetic map: Chunlei Su & David Sibley Mapping: Bindu Gajria & David Roos

Improved Genetic & Physical Maps A. Khan et al (2005) Nucl. Acids Res. 33:2980

A. Khan et al (2005) Nucl. Acids Res. 33:2980