Upload File

gbrowse – introduction

16
GBrowse – Introduction Developed by GMOD Generic Model Organism Database Generic G enome Browse r Web application to explore genomes Free software Goal: simplify & standardize MODs Model Organism Databases

Upload: palti

Post on 05-Feb-2016

26 views

Category:

Documents


0 download

Report

Tags:

DESCRIPTION

GBrowse – Introduction. Developed by GMOD Generic Model Organism Database Generic G enome Browse r Web application to explore genomes Free software Goal: simplify & standardize MODs Model Organism Databases. colored glyphs. GBrowse – Introduction. bird’s eye view. - PowerPoint PPT Presentation

TRANSCRIPT

Page 1: GBrowse – Introduction

GBrowse – Introduction

Developed by GMODGeneric Model Organism Database

Generic Genome Browser

Web application to explore genomes

Free software

Goal: simplify & standardize MODs Model Organism Databases

Page 2: GBrowse – Introduction

GBrowse – Introduction

bird’s eye view...

...or zoom in for details

colored glyphs

customize it

Page 3: GBrowse – Introduction

GBrowse – Examples Human GenomeSegmental DuplicationDatabase

Page 4: GBrowse – Introduction

GBrowse – Features

banner

description

tracks

cookies

instructions

search

overview

details

overview

region displayed

Page 5: GBrowse – Introduction

GBrowse – Features what’s

allowablefor searches

bookmark current view and settings

for re-visits to page

view Detail image in SVG format

restore standardsettings

Page 6: GBrowse – Introduction

GBrowse – Features

Gene symbolsGene IDsSequence IDsGenetic markersRelative nucleotide coordinatesAbsolute nucleotide coordinatesetc...

click

Page 7: GBrowse – Introduction

GBrowse – Features

pick-list

Page 8: GBrowse – Introduction

GBrowse – Installation

Apache

MySQL (recommended)

Perl

Standard Perl modulesCGI (2.56 or higher) GD (2.07 or higher) CGI::Session (4.03 or higher) DBI (any version) DBD::mysql (any version) Digest::MD5 (any version) Text::Shellwords (any version) Class::Base (any version)

Page 9: GBrowse – Introduction

BioPerlBio::Graphics Bio::DB::Das::Chado

Optional Perl modulesXML::Parser, XML::Writer, XML::Twig, XML::DOM

LWP Bio::Das

BioMOBY GD::SVG Bio::SCF File::Temp io-lib(v1.7+) Math::FFT Statistics::Descriptive Bio::PrimerDesigner, Math::Round, primer3

GBrowse – Installation

Page 10: GBrowse – Introduction

http://prdownloads.sourceforge.net/gmod

File: GBrowse-2.21.tar.gz

Extract: tar –xvzf GBrowse-2.21.tar.gz

Folder: cd GBrowse-2.21

GBrowse – Installation

http://prdownloads.sourceforge.net/gmod
http://prdownloads.sourceforge.net/gmod
Page 11: GBrowse – Introduction

http://prdownloads.sourceforge.net/gmod

File: GBrowse-2.21.tar.gz

Extract: tar –xvzf GBrowse-2.21.tar.gz

Folder: cd GBrowse-2.21

Run in terminal for unix system

perl Makefile.PL

make

make test (optional)

make install

GBrowse – Installation

http://prdownloads.sourceforge.net/gmod
http://prdownloads.sourceforge.net/gmod
Page 12: GBrowse – Introduction

perl Makefile.PL

HTDOCS : /var/www/

CONF: /etc/apache2/

CGIBIN: /usr/lib/cgi-bin

APACHE: /var/www/

GBrowse – Installation

Page 13: GBrowse – Introduction

Database – Preparations

mysql -uroot -ppassword -e 'create database yeast'

mysql -uroot -ppassword -e 'grant all privileges on yeast.* to me@localhost‘

mysql -uroot -ppassword -e 'grant file on *.* to me@localhost'

mysql -uroot -ppassword -e 'grant select on yeast.* to nobody@localhost‘

bp_bulk_load_gff.pl -d yeast –create sample_data/yeast_data.gff

bp_load_gff.pl -d yeast -fasta yeast.fasta.gz

bp_bulk_load_gff.pl -d yeast sample_data/yeast_data.gff

Page 14: GBrowse – Introduction

GBrowse – Configuration

[GENERAL] description = S. cerevisiae (via SGD Nov 2001) db_adaptor = Bio::DB::GFF db_args = -adaptor dbi::mysql

-dsn dbi:mysql:database=yeast;host=localhost aggregators = transcript alignment user = passwd = .[Genes] feature = gene:sgd glyph = generic bgcolor = yellow forwardcolor = yellow reversecolor = turquoise strand_arrow = 1 height = 6 description = 1 key = Named gene

Page 15: GBrowse – Introduction

GBrowse – Configuration

init_code = sub score_color { my $feature = shift; if ($feature->score > 50) { return 'red'; } else{ return 'green'; } } sub score_height { my $feature = shift; if ($feature->score > 50) { return 10; } else { return 5; } }

Page 16: GBrowse – Introduction

GBrowse – Configuration

[EST_ALIGNMENTS] glyph = generic bgcolor = \&score_color height = \&score_height


§1.1.1 INTRODUCTION: 1. INTRODUCTION

GBrowse at TAIR Philippe Lamesch TAIR curator. Seqviewer

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

Edinburgh Research Explorer · et al., 2005) for domain identification and GBrowse for genome browser delivery. Loading data into a Badger instance is straightforward (Fig. 1). First,

1. Introduction 1. Introduction 1. Introduction 1 ... · Introduction 1. Introduction 1. Introduction 1. Introduction 6061B0242401. The Phone Screen From the Phone screen, you can

JBrowse PAG 2017 - GMODgmod.org/mediawiki/images/e/e2/JBrowse_PAG_2017.pdf · Other GMOD Projects • GBrowse - “old school” Genome Browser, based on BioPerl • MAKER - Tool

R as a Web Service Introduction Introduction Introduction

Introduction - daks2k3a4ib2z.cloudfront.net€¦ · Introduction Establishedin1974MarbleHillFireplacesofferoneofthelargestandmostcomprehensiveselectionsof …

INTRODUCTION SPECIFICATIONS INTRODUCTION

Introduction to Logic Introduction

COSMIC GBrowse Visualising cancer mutations in genomic context Dave Beare [email protected] Cancer Genome Project Wellcome Trust Sanger Institute, Hinxton,

1. Introduction 10 - therackonline.com€¦ · 1. Introduction 10 - therackonline.com ... Introduction)

Introduction 1. Introduction

GBrowse Population Display and CMap SMBE 2009 Ben Faga

General introduction 1.1 Introduction

Systems Analysis I introduction I introduction. 2Systems Analysis - Introduction Contents Introduction Introduction 3 classic phases 3 classic phases

An Introduction for An Introduction for Introduction for ......An Introduction for An Introduction for Introduction for TeachersTeachersTeachers . exChange, Blackburn Cathedral’s

URBAN STREAM REHABILITATION. INTRODUCTION, OBJECTIVES & IMPACTS INTRODUCTION, OBJECTIVES & IMPACTS INTRODUCTION, OBJECTIVES & IMPACTS INTRODUCTION, OBJECTIVES

Introduction Introduction (ctnd.)

Introducción / Introduction / Introduction

Introduction | Introduction | Millennium Serials · 2018. 4. 17. · MARC Display | Print | Introduction | Millennium Serials INTRODUCTION Introduction This tutorial introduces the

Introduction€¦ · Introduction ThisdocumentprovidesinformationabouttheIOSXEsoftwarereleasefortheCiscoNCS4201andCisco …

 · Contents INTRODUCTION Introduction

View Genomes in GBrowse · 2020-04-20 · annotations of Herpesviridae and Poxviridae viruses •Select and customize annotations using tracks •Upload and incorporate your own unpublished

INTRODUCTIONS (LEADS) Creative introduction Action introduction Dialogue introduction Personal introduction Question introduction Quotation introduction

Introduction to Transducers, Introduction to Transducers ... on... · Introduction to Transducers, Introduction to Transducers, Sensors and ActuatorsSensors and Actuators Introduction

Introduction to introduction to introduction to … Optimization

Gallus GBrowse: a unified genomic database for the chicken

JBrowse programming for biology 2016gmod.org/mediawiki/images/1/13/JBrowse_programming_for_biolog… · Other GMOD Projects • GBrowse - “old school” Genome Browser, based on

GBrowse – Introduction Developed by GMOD Generic Model Organism Database Generic Genome Browser Web application to explore genomes Free software Goal:

1 Introduction t 1. Introduction to Nanotechnology - UFAMhome.ufam.edu.br/berti/nanomateriais/Introduction to Nanotechnology... · Introduction t 1. Introduction to Nanotechnology

Running GBrowse and DAS/1 on GUS Haiming Wang Jessica Kissinger Laboratory, Genetics C210 University of Georgia GUS Workshop August 8, 2005

Introduction - University of Cambridge · Introduction. Introduction

PRODUCT INTRODUCTION Company Introduction

Introduction Introduction Introduction Introduction