Copyright OpenHelix. No use or reproduction without express written consent1

TAIR: The Arabidopsis Information Resource A resource for Arabidopsis thaliana genetic and molecular data Materials prepared by: Jennifer Williams, Ph.D. Updated: Q Version 1

Copyright OpenHelix. No use or reproduction without express written consent3 TAIR Agenda Introduction and Credits Searches Basic Browsers Genome Browser AraCyc Metabolic Pathway Viewer Sequence Alignment Tools Additional Tools Summary Exercises TAIR:

TAIR Introduction Copyright OpenHelix. No use or reproduction without express written consent4 TAIR: comprehensive, current information about Arabidopsis thaliana Complete genome sequence, gene structure, metabolism, maps, markers, publications and more Updated regularly

TAIR Credits Copyright OpenHelix. No use or reproduction without express written consent5

TAIR Publications Copyright OpenHelix. No use or reproduction without express written consent6

Many Tools & Options From TAIR Homepage Copyright OpenHelix. No use or reproduction without express written consent7 Stocks - Arabidopsis Biological Resource Center (ABRC) tools Portals - resources and information organized by topic Download - TAIR ftp site for downloading various materials Submit - where you can contribute to TAIR efforts News - several methods of accessing info, including joining newsgroups and posting job ads

Many Tools & Options From TAIR Homepage Copyright OpenHelix. No use or reproduction without express written consent8 Search by: Genes, DNA/Clones, Ecotypes, Keywords, GO, History, Markers, Microarray, etc. Textpresso: new text-mining system Tools: GBrowser, Seqviewer, Mapviewer, Metabolic Pathways, Sequence Alignments, and more!

TAIR Online Help Copyright OpenHelix. No use or reproduction without express written consent9 Click Help Search Tutorials FAQ Quick Start Tools Glossary

Copyright OpenHelix. No use or reproduction without express written consent10 TAIR Agenda Introduction and Credits Searches Basic Browsers Genome Browser AraCyc Metabolic Pathway Viewer Sequence Alignment Tools Additional Tools Summary Exercises TAIR:

Searches Copyright OpenHelix. No use or reproduction without express written consent11 keyword Click

Search Overview Copyright OpenHelix. No use or reproduction without express written consent12 Click Many specific searches available on the Search Overview page Our example will be the Genes search

Gene Search Options Copyright OpenHelix. No use or reproduction without express written consent13 Select

More Gene Search Options Copyright OpenHelix. No use or reproduction without express written consent14 Select

Restricting Your Gene Search & Output Options Copyright OpenHelix. No use or reproduction without express written consent15 Select

Gene Search Example Copyright OpenHelix. No use or reproduction without express written consent16 Select Click

Gene Search Results Copyright OpenHelix. No use or reproduction without express written consent17

Copyright OpenHelix. No use or reproduction without express written consent18 TAIR Agenda Introduction and Credits Searches Basic Browsers Genome Browser AraCyc Metabolic Pathway Viewer Sequence Alignment Tools Additional Tools Summary Exercises TAIR:

Basic Browsers Copyright OpenHelix. No use or reproduction without express written consent19 Click

ABRC Browser Copyright OpenHelix. No use or reproduction without express written consent20 Mutants Transgenic lines Genomic libraries Clones

2010 Projects Copyright OpenHelix. No use or reproduction without express written consent21 Click

Monsanto SNP and Ler Collections Copyright OpenHelix. No use or reproduction without express written consent22 Click

Gene Families Copyright OpenHelix. No use or reproduction without express written consent23 Click

Gene Symbols Copyright OpenHelix. No use or reproduction without express written consent24 Click

Ontologies/Keywords Copyright OpenHelix. No use or reproduction without express written consent25 Click Enter terms

Archived e-Journals Copyright OpenHelix. No use or reproduction without express written consent26 Click

Copyright OpenHelix. No use or reproduction without express written consent27 TAIR Agenda Introduction and Credits Searches Basic Browsers Genome Browser AraCyc Metabolic Pathway Viewer Sequence Alignment Tools Additional Tools Summary Exercises TAIR:

GBrowse Access Copyright OpenHelix. No use or reproduction without express written consent28 Click

GBrowse Search Copyright OpenHelix. No use or reproduction without express written consent29 Click

GBrowse Overview and Details Copyright OpenHelix. No use or reproduction without express written consent30 Locus Protein cDNAs Transposons Polymorphisms

GBrowse VISTA Plots Copyright OpenHelix. No use or reproduction without express written consent31

GBrowse Tracks Copyright OpenHelix. No use or reproduction without express written consent32 Click

GBrowse Customized Details Copyright OpenHelix. No use or reproduction without express written consent33

Copyright OpenHelix. No use or reproduction without express written consent34 TAIR Agenda Introduction and Credits Searches Basic Browsers Genome Browser AraCyc Metabolic Pathway Viewer Sequence Alignment Tools Additional Tools Summary Exercises TAIR:

AraCyc Metabolic Pathway Tool Access Copyright OpenHelix. No use or reproduction without express written consent35 Click

AraCyc Metabolic Pathway Tool Homepage Copyright OpenHelix. No use or reproduction without express written consent36 Search Click Intro Browse Submit Release

AraCyc Metabolic Pathway Search Copyright OpenHelix. No use or reproduction without express written consent37 Select Click

AraCyc Metabolic Pathway Browser Copyright OpenHelix. No use or reproduction without express written consent38 Click

AraCyc Metabolic Pathway Browser Options Copyright OpenHelix. No use or reproduction without express written consent39 Click

Pathway Information Page-Top Copyright OpenHelix. No use or reproduction without express written consent40

Pathway Information Page-Bottom Copyright OpenHelix. No use or reproduction without express written consent41

Copyright OpenHelix. No use or reproduction without express written consent42 TAIR Agenda Introduction and Credits Searches Basic Browsers Genome Browser AraCyc Metabolic Pathway Viewer Sequence Alignment Tools Additional Tools Summary Exercises TAIR:

Sequence Alignment Tools Copyright OpenHelix. No use or reproduction without express written consent43 Click

BLAST Search Copyright OpenHelix. No use or reproduction without express written consent44 Click Select

BLAST Options Copyright OpenHelix. No use or reproduction without express written consent45 Click Select

Submitting Your BLAST Search Copyright OpenHelix. No use or reproduction without express written consent46 Insert sequence here Click

BLAST Results Copyright OpenHelix. No use or reproduction without express written consent47

Copyright OpenHelix. No use or reproduction without express written consent48 TAIR Agenda Introduction and Credits Searches Basic Browsers Genome Browser AraCyc Metabolic Pathway Viewer Sequence Alignment Tools Additional Tools Summary Exercises TAIR:

Additional Tools: Bulk Data Retrieval Copyright OpenHelix. No use or reproduction without express written consent49 Click

Bulk Data Retrieval Tool Copyright OpenHelix. No use or reproduction without express written consent50 Click

Bulk Data Retrieval Tool: Gene Descriptions Copyright OpenHelix. No use or reproduction without express written consent51 Search Options Output Options

Additional Tools Copyright OpenHelix. No use or reproduction without express written consent52 Click

Chromosomal Map Tool Copyright OpenHelix. No use or reproduction without express written consent53 Your results

Restriction Analysis Tool Copyright OpenHelix. No use or reproduction without express written consent54

Restriction Analysis Results-Top Copyright OpenHelix. No use or reproduction without express written consent55 Enzymes used

Restriction Analysis Results-Bottom Copyright OpenHelix. No use or reproduction without express written consent56 Key Enzymes that don’t cut

Copyright OpenHelix. No use or reproduction without express written consent57 TAIR Agenda Introduction and Credits Searches Basic Browsers Genome Browser AraCyc Metabolic Pathway Viewer Sequence Alignment Tools Additional Tools Summary Exercises TAIR:

Summary Comprehensive data for Arabidopsis thaliana Freely available to the public and updated regularly Copyright OpenHelix. No use or reproduction without express written consent58

Many Topics Easily searchable topics range from molecular biology and biochemistry to classical genetics Copyright OpenHelix. No use or reproduction without express written consent59

Copyright OpenHelix. No use or reproduction without express written consent60 TAIR Agenda Introduction and Credits Searches Basic Browsers Genome Browser AraCyc Metabolic Pathway Viewer Sequence Alignment Tools Additional Tools Summary Exercises TAIR:

Copyright OpenHelix. No use or reproduction without express written consent61