1 popcorn: project portal for corn a set of project and sequence-indexed data searching resources ()...

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POPcorn: Project Portal for cornA set of project and sequence-indexed

data searching resources

(http://popcorn.maizegdb.org)

Jack M. GardinerPoster P897

POPcorn: Project Portal for corn http://popcorn.maizegdb.org

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http://popcorn.maizegdb.orghttp://popcorn.maizegdb.org

A set of project and sequence-indexed data searching resources

POPcorn: Project Portal for corn www.popcorn.maizegdb.org

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Project Objectives:

• Difficult to find all online resources relevant to one’s research

• Project Search

Project Objectives:

• Difficult to find all online resources relevant to one’s research

• Project Search

POPcorn: Project Portal for corn www.maizegdb.org/POPcorn

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Project Objectives:• Difficult to find all online resources relevant to one’s research

• Project Search• Repeated BLAST searches at multiple sites

• POPcorn BLAST

Project Objectives:• Difficult to find all online resources relevant to one’s research

• Project Search• Repeated BLAST searches at multiple sites

• POPcorn BLAST


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Project Objectives:

• Difficult to find all online resources relevant to one’s research• Project Search

• Repeated BLAST searches at multiple sites• POPcorn BLAST

• Sequence-indexed data can be challenging to search• Sequence-Indexed Data Search

Project Objectives:





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Project Objectives:




• Data and web resources can disappear after project completion• Processes and scripts to migrate data to MaizeGDB

Project Objectives:




• Data and web resources can disappear after project completion• Processes and scripts to migrate data to MaizeGDB


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Project Search• Database of maize research projects and online resources• Hand-curated and updated monthly; 97 projects, 128 resources

Project Search• Database of maize research projects and online resources• Hand-curated and updated monthly; 97 projects, 128 resources


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Project Search•Database of maize research projects and online resources• Hand-curated and updated monthly; 97 projects, 128 resources• We need your help!

• submit projects not in our database• send us corrections

Project Search•Database of maize research projects and online resources• Hand-curated and updated monthly; 97 projects, 128 resources• We need your help!



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Project Search•Database of maize research projects and online resources• Hand-curated and updated monthly; 97 projects, 128 resources• Information presented for each project and resource• We need your help!


• Types of projects and resources: • just about everything that is relevant to maize• … except cultural, archeological and educational; those go into PGROP at PlantGDB (http://www.plantgdb.org/PGROP/)

Project Search•Database of maize research projects and online resources• Hand-curated and updated monthly; 97 projects, 128 resources• Information presented for each project and resource• We need your help!


• Types of projects and resources: • just about everything that is relevant to maize• … except cultural, archeological and educational; those go into PGROP at PlantGDB (http://www.plantgdb.org/PGROP/)


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•Two options for searching with a sequence•Simple sequence to sequence search (BLAST)•Sequenced index search (access biological resources associated with a sequence)

•Two options for searching with a sequence•Simple sequence to sequence search (BLAST)•Sequenced index search (access biological resources associated with a sequence)


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•BLAST against target sequence at multiple websites using Web Services•Results can be returned via email•BLAST against target sequence at multiple websites using Web Services•Results can be returned via email


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•BLAST against target sequence at multiple websites using Web Services•Results can be returned via email•Contact us to add your target sequence or to set up a similar service

•BLAST against target sequence at multiple websites using Web Services•Results can be returned via email•Contact us to add your target sequence or to set up a similar service


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Sequence-indexed data search• Carries out complex searches• One or more searches at once

Sequence-indexed data search• Carries out complex searches• One or more searches at once


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An example: steps taken to find a UniformMu stock containing a given mutation.

1. BLAST query sequence against NCBI GSS 2. Parse definition line to get UniformMu locus name3. Get LOCUS record at MaizeGDB4. Get VARIATION record(s) for that LOCUS at MaizeGDB5. Get UniformMu STOCK records for each VARIATION at MaizeGDB6. Construct links to MGC Stock Center for each stock found.

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An example: steps taken to find a UniformMu stock containing a given mutation.

1. BLAST query sequence against NCBI GSS 2. Parse definition line to get UniformMu locus name3. Get LOCUS record at MaizeGDB4. Get VARIATION records for that LOCUS at MaizeGDB5. Get UniformMu STOCK records for each VARIATION at MaizeGDB6. Construct links to MGC Stock Center for each stock found.

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Select a target

databaseInput your sequence (split files larger than 20MB)

Provide some information about your data

Submit!

uBLAST

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Monitor progress of your job

You will receive an e-mail when your job is complete

uBLAST

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Check your alignment on the MaizeGDB.org genome browser

If the results look correct, submit to MaizeGDB.org

uBLAST

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CViT – Chromosome Viewing ToolDisplays features on chromosomes (linkage groups, pseudomolecules, chromosome arms, et cetera)

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CViT – Chromosome Viewing Tool

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POPcornPrincipal Investigator: Carolyn Lawrence (USDA-ARS)Co-Principal Investigator: Taner Sen (USDA-ARS)Solution/Application Architect: Ethy Cannon (Iowa State)Programmer Analyst: Scott Birkett (Iowa State)Programmer Analyst: Bremen Braun (USDA-ARS)Curator: Jack Gardiner (Iowa State)

POPcornPrincipal Investigator: Carolyn Lawrence (USDA-ARS)Co-Principal Investigator: Taner Sen (USDA-ARS)Solution/Application Architect: Ethy Cannon (Iowa State)Programmer Analyst: Scott Birkett (Iowa State)Programmer Analyst: Bremen Braun (USDA-ARS)Curator: Jack Gardiner (Iowa State)

MaizeGDB/POPcorn team

Poster P897

1 popcorn: project portal for corn a set of project and sequence-indexed data searching resources ()...

Documents

project portal

set of project

resources http

search blast

sequence slide

maizegdb project objectives

online resources relevant

corn http