Comparative Genomics with GBrowse_syn Sheldon McKay.

Slides:

Advertisements

Similar presentations

Web Apollo Resources at the National Agricultural Library Christopher Childers NAL ARS USDA i5k.nal.usda.gov.

Advertisements

Structural Biology and Biocomputing Programme 1 Osvaldo Graña, CNIO Distributed Annotation System (DAS) part I Osvaldo Graña VIII.

InterPro/prosite UCSC Genome Browser Exercise 3. Turning information into knowledge  The outcome of a sequencing project is masses of raw data  The.

Comparative Genomics Bio Informatics Scott Gulledge.

Genomic Database - Ensembl Ka-Lok Ng Department of Bioinformatics Asia University.

We are developing a web database for plant comparative genomics, named Phytome, that, when complete, will integrate organismal phylogenies, genetic maps.

WormBase Workshop: 2015 International C. elegans Meeting Tools & Resources InterMine / WormMine – Chris Grove JBrowse – Scott Cain The WormBase Ontology.

GMOD: Building Blocks for a Model Organism System Database Lincoln Stein, CSHL.

WormBase: A Resource for the Biology & Genome of C. elegans Lincoln D. Stein.

WebGBrowse A Web Server for GBrowse Configuration Ram Podicheti B.V.Sc. & A.H. (D.V.M.), M.S. Staff Scientist – Bioinformatics Center for Genomics and.

GeVab: Genome Variation Analysis Browsing Server Korean BioInformation Center, KRIBB InCoB2009 KRIBB

Jing Yu 1, Sook Jung 1, Chun-Huai Cheng 1, Stephen Ficklin 1, Taein Lee 1, Ping Zheng 1, Don Jones 2, Richard Percy 3, Dorrie Main 1 1. Washington State.

TAIR, PMN, SGN and Gramene workshop Focus on comparative genomics and new tools Philippe Lamesch, A. S. Karthikeyan, Aureliano Bombarely Gomez, Pankaj.

Comparative Genomics Tools in GMOD GMOD.org Dave Clements 1, Sheldon McKay 2, Ken Youns-Clark 2, Ben Faga 3, Scott Cain 4, and the GMOD Consortium 1 National.

05/04/2005 Informatics Meeting C. elegans – “Back To The Future”. Paul Davis (aka Huey)

How many vegetarians are there? And... Before I do anything...

Andy Conley 3/26/ James Kent. Know that name. He is one of greatest, perhaps the greatest, bioinformatics programmers ever. He was deeply involved.

Visualising NGS data in GBrowse 2 August 2009 GMOD Meeting 6-7 August 2009 Dave Clements GMOD Help Desk National Evolutionary Synthesis Center (NESCent)

GMOD/GBrowse_syn Sheldon McKay iPlant Collaborative DNA Learning Center Cold Spring Harbor Laboratory.

GMOD: Managing Genomic Data from Emerging Model Organisms Dave Clements 1, Hilmar Lapp 1, Brian Osborne 2, Todd J. Vision 1 1 National Evolutionary Synthesis.

Browsing the Genome Using Genome Browsers to Visualize and Mine Data.

Got genom e? Community Meetings GMOD.org The GMOD community meets semi- annually to discuss GMOD components, best practices,

Flexible genome retrieval for supporting in-silico studies of endobacteria-AMFs S. Montani 1, G. Leonardi 1, S. Ghignone 2, L. Lanfranco 2 1 Dipartimento.

Construction of Substitution Matrices

The generic Genome Browser (GBrowse) A combination database and interactive web page for manipulating and displaying annotations on genomes Developed by.

Web Databases for Drosophila Introduction to FlyBase and Ensembl Database Wilson Leung6/06.

Managing Next Generation Sequence Data with GMOD Dave Clements 1, Scott Cain 2, Paul Hohenlohe 3, Nicholas Stiffler 3, Paul Etter 3, Eric Johnson 3, William.

GMOD Meeting August 6-7, 2009 Oxford, UK Scott Cain, PhD. GMOD Project Coordinator Ontario Institute for Cancer Research

GMOD/GBrowse_syn Sheldon McKay Reactome Ontario Institute for Cancer Research.

GBrowse Population Display and CMap SMBE 2009 Ben Faga.

Orthology & Paralogy Alignment & Assembly Alastair Kerr Ph.D. [many slides borrowed from various sources]

Curation Tools Gary Williams Sanger Institute. SAB 2008 Gene curation – prediction software Gene prediction software is good, but not perfect. Out of.

Web Databases for Drosophila An introduction to web tools, databases and NCBI BLAST Wilson Leung08/2015.

Orthologs, Diseases, and Interactions Norie de la Cruz.

Copyright OpenHelix. No use or reproduction without express written consent1.

tools for synteny analysis

Stein Lab In-House Symposium Lincoln Sends His Regrets.

By Michael Han Sanger Wormbase Group SAB 2008 Comparative Genomics with.

Web Apollo Resources at the National Agricultural Library Christopher Childers NAL ARS USDA i5k.nal.usda.gov.

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

Copyright OpenHelix. No use or reproduction without express written consent1.

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.

GBrowse: Generic Genome Browser May 2003 Update Lincoln Stein, CSHL.

IMDB: A Generic Insertional Mutagenesis Database Xiaokang Pan and Lincoln Stein Cold Spring Harbor Laboratory.

Accessing and visualizing genomics data

Introductory Phylogenetic Workflows in the Discovery Environment Sheldon McKay iPlant Collaborative, DNALC, Cold Spring Harbor Laboratory Feb 8, 2012.

GMOD/GBrowse_syn Sheldon McKay iPlant Collaborative DNA Learning Center Cold Spring Harbor Laboratory.

The State of GMOD March 2011 GMOD Meeting US National Evolutionary Synthesis Center (NESCent) 5 March 2011 Sponsored by Scott Cain GMOD Project Coordinator.

The Bovine Genome Database Abstract The Bovine Genome Database (BGD, facilitates the integration of bovine genomic data. BGD is.

Canadian Bioinformatics Workshops

Comparative Genomics.

Behavior and Phenotype in GMOD Natural Diversity in GMOD

Genome Browsers.

Bioinformatics Tools for Comparative Genomics of Vectors

University of Pittsburgh

TSS Annotation Workflow

GEP Annotation Workflow

The Celera Genome Browser: A Tool for Visualizing and Annotating the Human Genome

INFORMATION FLOW AARTHI & NEHA.

Strategies for annotation of a genome

Ensembl Genome Repository.

got genome? Community Meetings Databases Training GMOD.org

Identify D. melanogaster ortholog

Plant and Animal Genome XVIII

TAMU Bovine QTL db and viewer

for the Cotton Community

Updates and Future Direction

Yating Liu July 2018 G-OnRamp workshop

1. C. briggsae sequence curation 2. SNP data handling

Follow-up from last night: XSEDE credits

Presentation transcript:

Comparative Genomics with GBrowse_syn Sheldon McKay

How to get comparative genomics data How to view the data with GBrowse_syn Example uses

Hierarchical Genome Alignment Strategy Mask repeats (RepeatMasker [97] and Tandem Repeats Finder, nmerge, etc Identify orthologous regions (MERCATOR, orthocluster, etc) Nucleotide-level alignment (PECAN, MAVID, etc) Further processing (GERT) Gbrowse_syn GBrowse Raw genomic sequences

SynView Sybil SynBrowse CMAP GBrowse UCSC-style conservation tracks

What is GBrowse_syn? Part of the Generic Genome Browser Package (GBrowse) A graphical multiple sequence alignment viewer Superimposes sequence alignment data on genes and other sequence features Compares two or more species to a central reference species

GBrowse-like interface

GBrowse Databases* *.syn or *.conf *.synconf GBrowse_syn alignment database GBrowse_syn Species config. Master config.

GBrowse_syn Architecture [GBrowse]

All in one view

How to use Insertions/Deletion data

Tracking Indels with grid lines

Evolution of Gene Structure

Very (un)popular popup balloons

Comparing gene annotations:

C. elegans C. briggsae C. remanei

Visual inspection of an assembly Not bad Done Needs work

Putative gene loss

Chaining Alignments

Small inversions

Future Improvements “On the fly” sequence alignment view (definitely) AJAX-based image configuration (probably) 3D image rendering? (maybe) Suggestions?

Documentation:

Acknowledgements Lincoln Stein Todd Vision Dave Clements Scott Cain Jason Stajich Michael Han WormBase Curators Washington University Genome Sequencing Center