Presentation is loading. Please wait.

Presentation is loading. Please wait.

Maize Genome Project Shiran Pasternak January 13, 2006 Gramene SAB Meeting San Diego, CA Shiran Pasternak January 13, 2006 Gramene SAB Meeting San Diego,

PublishEllen Melton Modified over 8 years ago

Similar presentations

Presentation on theme: "Maize Genome Project Shiran Pasternak January 13, 2006 Gramene SAB Meeting San Diego, CA Shiran Pasternak January 13, 2006 Gramene SAB Meeting San Diego,"— Presentation transcript:

1 Maize Genome Project Shiran Pasternak January 13, 2006 Gramene SAB Meeting San Diego, CA Shiran Pasternak January 13, 2006 Gramene SAB Meeting San Diego, CA

2 3 year sequencing effort Funded November, 2005 Objectives Sequence the maize genespace Genic and regulatory regions Finish 721 contigs: 1 in 100,000 error rate Anchor to physical and genetic maps Maize Genome Project

3 Arizona Genome Institute (AGI) Mapping Washington University at St. Louis (WU) Sequencing Cold Spring Harbor Laboratory (CSHL) Analysis and Annotation Project Participants

4 Institutional Layout

5 Annotation Visualization CSHL Functions

6 Annotation Internal Public

7 Prefinishing: Automated Enrich BAC assemblies with AutoFinish ‘Do Not Finish’ repeat tags Finishing: Manual Tag mRNA and ESTs to target problematic regions Internal Annotation

8 Iteratively redefine gene boundaries Provide new knowledge on maize genome Communicate status of the project Public Annotation

9 Annotation Pipeline Gramene-Ensembl Whole genome alignment to rice ab initio gene prediction with Fgenesh Evidence-based gene prediction Repeat analysis Full annotation on nearly finished BACs

10 Gramene and Ensembl Browser Existing: Contigs, Genes, Synteny CMap Views Whole genome alignment Sequencing status of BACs & Contigs Other track suggestions? Visualization

11 ContigView

12 Synteny View * against Rice

13 GeneView

14 New Views

15 Infrastructure Hardware 2 servers, forthcoming node cluster Dedicated architecture Genome browser Database schemata Annotation pipeline

16 Data Releases Ongoing annotation updates (weekly) Repeats Gene models Infrequent genome builds (yearly?) Orthologs Syntenic Loci

17 Release Timeline March, 2006 Annotation Pipeline Launch of Weekly Updates July, 2006 January, 2007

18 Impact on Gramene Cost: $0 Maize browser will link to Gramene content Evolving requirements

19 Staffing Principal Investigators Rick Wilson (WU) Sandra Clifton (WU) Pat Schnable (IA) Srinivas Aluru (IA) Rod Wing (AGI) Rob Martienssen (CSHL) Dick McCombie (CSHL) Doreen Ware (CSHL) Lincoln Stein (CSHL) CSHL Team Shiran Pasternak (Lead) Apurva Narechania (Software) Ben Faga (CMap) Unnamed Data Analyst Unnamed Software Developer

20 Thanks!

Download ppt "Maize Genome Project Shiran Pasternak January 13, 2006 Gramene SAB Meeting San Diego, CA Shiran Pasternak January 13, 2006 Gramene SAB Meeting San Diego,"

Similar presentations

Mo17 shotgun project Goal: sequence Mo17 gene space with inexpensive new technologies Datasets in progress: Four-phases of 454-FLX sequencing to max of.

Mo17 shotgun project Goal: sequence Mo17 gene space with inexpensive new technologies Datasets in progress: Four-phases of 454-FLX sequencing to max of.
Sequencing the Maize Genome Maize Genome Sequencing Consortium

Sequencing the Maize Genome Maize Genome Sequencing Consortium
Sequencing the Maize (B73) Genome

Sequencing the Maize (B73) Genome
Annotation and Visualization Doreen Ware. Project Challenges Rapidly growing sequence data Full annotation of all clones New high-performance computing.

Annotation and Visualization Doreen Ware. Project Challenges Rapidly growing sequence data Full annotation of all clones New high-performance computing.
Accurate Assembly of Maize BACs Patrick S. Schnable Srinivas Aluru Iowa State University.

Accurate Assembly of Maize BACs Patrick S. Schnable Srinivas Aluru Iowa State University.
Maize Genetics, Genomics, Bioinformatics workshop

Maize Genetics, Genomics, Bioinformatics workshop
Toward a Better Understanding of Cereal Genome Evolution Through Ensembl Compara 1111, Apurva Narechania 1, Joshua Stein 1, William Spooner 1, Sharon Wei.

Toward a Better Understanding of Cereal Genome Evolution Through Ensembl Compara 1111, Apurva Narechania 1, Joshua Stein 1, William Spooner 1, Sharon Wei.
Stein Lab In-House Symposium 2002. The Plan  Overview of my lab’s activities  Detailed look at the Gramene Database  Run out of time  Talk really.

Stein Lab In-House Symposium The Plan  Overview of my lab’s activities  Detailed look at the Gramene Database  Run out of time  Talk really.
Genome Annotation using MAKER-P at iPlant Collaboration with Mark Yandell Lab (University of Utah) www.yandell-lab.org iPlant: Josh Stein (CSHL) Matt Vaughn.

Genome Annotation using MAKER-P at iPlant Collaboration with Mark Yandell Lab (University of Utah) iPlant: Josh Stein (CSHL) Matt Vaughn.
Annotating a Scarlet Runner Bean genome fragment put together by shotgun sequencing Scarlet Runner ean Max Bachour.

Annotating a Scarlet Runner Bean genome fragment put together by shotgun sequencing Scarlet Runner ean Max Bachour.
Some Jolly Fun with Barley ESTs David Marshall & All the Folks in Computational Biology.

Some Jolly Fun with Barley ESTs David Marshall & All the Folks in Computational Biology.
Gramene Scientific Advisory Board Meeting January 2005.

Gramene Scientific Advisory Board Meeting January 2005.
Gramene Comparative & Phylogenomics Resources for Plants Joshua C. Stein 1, William Spooner 1, Sharon Wei 1, Liya Ren 1, Doreen Ware 1,2 1 Cold Spring.

Gramene Comparative & Phylogenomics Resources for Plants Joshua C. Stein 1, William Spooner 1, Sharon Wei 1, Liya Ren 1, Doreen Ware 1,2 1 Cold Spring.
Lecture 2.21 Retrieving Information: Using Entrez.

Lecture 2.21 Retrieving Information: Using Entrez.
Genomic Database - Ensembl Ka-Lok Ng Department of Bioinformatics Asia University.

Genomic Database - Ensembl Ka-Lok Ng Department of Bioinformatics Asia University.
How to access genomic information using Ensembl August 2005.

How to access genomic information using Ensembl August 2005.
Sequence Analysis. Today How to retrieve a DNA sequence? How to search for other related DNA sequences? How to search for its protein sequence? How to.

Sequence Analysis. Today How to retrieve a DNA sequence? How to search for other related DNA sequences? How to search for its protein sequence? How to.
2013 iPlant workshop Marcela Karey Monaco. 2013 What is Gramene? An integrated plant reference genome resource Comparative genomics hub of data & tools.

2013 iPlant workshop Marcela Karey Monaco What is Gramene? An integrated plant reference genome resource Comparative genomics hub of data & tools.
Genome sequencing. Vocabulary Bac: Bacterial Artificial Chromosome: cloning vector for yeast Pac, cosmid, fosmid, plasmid: cloning vectors for E. coli.

Genome sequencing. Vocabulary Bac: Bacterial Artificial Chromosome: cloning vector for yeast Pac, cosmid, fosmid, plasmid: cloning vectors for E. coli.
Genome Annotation BCB 660 October 20, 2011. From Carson Holt.

Genome Annotation BCB 660 October 20, From Carson Holt.

Similar presentations

Ads by Google