1 popcorn: project portal for corn a set of project and sequence-indexed data searching resources ()...
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![Page 1: 1 POPcorn: Project Portal for corn A set of project and sequence-indexed data searching resources () Jack M. Gardiner Poster](https://reader035.vdocuments.net/reader035/viewer/2022062618/5514a32055034640138b4a08/html5/thumbnails/1.jpg)
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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
![Page 2: 1 POPcorn: Project Portal for corn A set of project and sequence-indexed data searching resources () Jack M. Gardiner Poster](https://reader035.vdocuments.net/reader035/viewer/2022062618/5514a32055034640138b4a08/html5/thumbnails/2.jpg)
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
![Page 3: 1 POPcorn: Project Portal for corn A set of project and sequence-indexed data searching resources () Jack M. Gardiner Poster](https://reader035.vdocuments.net/reader035/viewer/2022062618/5514a32055034640138b4a08/html5/thumbnails/3.jpg)
POPcorn: Project Portal for corn www.popcorn.maizegdb.org
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![Page 4: 1 POPcorn: Project Portal for corn A set of project and sequence-indexed data searching resources () Jack M. Gardiner Poster](https://reader035.vdocuments.net/reader035/viewer/2022062618/5514a32055034640138b4a08/html5/thumbnails/4.jpg)
POPcorn: Project Portal for corn http://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
![Page 5: 1 POPcorn: Project Portal for corn A set of project and sequence-indexed data searching resources () Jack M. Gardiner Poster](https://reader035.vdocuments.net/reader035/viewer/2022062618/5514a32055034640138b4a08/html5/thumbnails/5.jpg)
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
![Page 6: 1 POPcorn: Project Portal for corn A set of project and sequence-indexed data searching resources () Jack M. Gardiner Poster](https://reader035.vdocuments.net/reader035/viewer/2022062618/5514a32055034640138b4a08/html5/thumbnails/6.jpg)
POPcorn: Project Portal for corn http://popcorn.maizegdb.org
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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:
• 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
![Page 7: 1 POPcorn: Project Portal for corn A set of project and sequence-indexed data searching resources () Jack M. Gardiner Poster](https://reader035.vdocuments.net/reader035/viewer/2022062618/5514a32055034640138b4a08/html5/thumbnails/7.jpg)
POPcorn: Project Portal for corn http://popcorn.maizegdb.org
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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
• Data and web resources can disappear after project completion• Processes and scripts to migrate data to MaizeGDB
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
• Data and web resources can disappear after project completion• Processes and scripts to migrate data to MaizeGDB
![Page 8: 1 POPcorn: Project Portal for corn A set of project and sequence-indexed data searching resources () Jack M. Gardiner Poster](https://reader035.vdocuments.net/reader035/viewer/2022062618/5514a32055034640138b4a08/html5/thumbnails/8.jpg)
POPcorn: Project Portal for corn http://popcorn.maizegdb.org
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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
![Page 9: 1 POPcorn: Project Portal for corn A set of project and sequence-indexed data searching resources () Jack M. Gardiner Poster](https://reader035.vdocuments.net/reader035/viewer/2022062618/5514a32055034640138b4a08/html5/thumbnails/9.jpg)
POPcorn: Project Portal for corn http://popcorn.maizegdb.org
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POPcorn: Project Portal for corn http://popcorn.maizegdb.org
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POPcorn: Project Portal for corn http://popcorn.maizegdb.org
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![Page 12: 1 POPcorn: Project Portal for corn A set of project and sequence-indexed data searching resources () Jack M. Gardiner Poster](https://reader035.vdocuments.net/reader035/viewer/2022062618/5514a32055034640138b4a08/html5/thumbnails/12.jpg)
POPcorn: Project Portal for corn http://popcorn.maizegdb.org
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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!
• submit projects not in our database• send us corrections
![Page 13: 1 POPcorn: Project Portal for corn A set of project and sequence-indexed data searching resources () Jack M. Gardiner Poster](https://reader035.vdocuments.net/reader035/viewer/2022062618/5514a32055034640138b4a08/html5/thumbnails/13.jpg)
POPcorn: Project Portal for corn http://popcorn.maizegdb.org
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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!
• submit projects not in our database• send us corrections
• 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!
• submit projects not in our database• send us corrections
• 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/)
![Page 14: 1 POPcorn: Project Portal for corn A set of project and sequence-indexed data searching resources () Jack M. Gardiner Poster](https://reader035.vdocuments.net/reader035/viewer/2022062618/5514a32055034640138b4a08/html5/thumbnails/14.jpg)
POPcorn: Project Portal for corn http://popcorn.maizegdb.org
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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)
![Page 15: 1 POPcorn: Project Portal for corn A set of project and sequence-indexed data searching resources () Jack M. Gardiner Poster](https://reader035.vdocuments.net/reader035/viewer/2022062618/5514a32055034640138b4a08/html5/thumbnails/15.jpg)
POPcorn: Project Portal for corn http://popcorn.maizegdb.org
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POPcorn: Project Portal for corn http://popcorn.maizegdb.org
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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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POPcorn: Project Portal for corn http://popcorn.maizegdb.org
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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
![Page 18: 1 POPcorn: Project Portal for corn A set of project and sequence-indexed data searching resources () Jack M. Gardiner Poster](https://reader035.vdocuments.net/reader035/viewer/2022062618/5514a32055034640138b4a08/html5/thumbnails/18.jpg)
POPcorn: Project Portal for corn http://popcorn.maizegdb.org
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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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POPcorn: Project Portal for corn http://popcorn.maizegdb.org
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POPcorn: Project Portal for corn http://popcorn.maizegdb.org
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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POPcorn: Project Portal for corn http://popcorn.maizegdb.org
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.
![Page 22: 1 POPcorn: Project Portal for corn A set of project and sequence-indexed data searching resources () Jack M. Gardiner Poster](https://reader035.vdocuments.net/reader035/viewer/2022062618/5514a32055034640138b4a08/html5/thumbnails/22.jpg)
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POPcorn: Project Portal for corn http://popcorn.maizegdb.org
Select a target
databaseInput your sequence (split files larger than 20MB)
Provide some information about your data
Submit!
uBLAST
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POPcorn: Project Portal for corn http://popcorn.maizegdb.org
Monitor progress of your job
You will receive an e-mail when your job is complete
uBLAST
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POPcorn: Project Portal for corn http://popcorn.maizegdb.org
Check your alignment on the MaizeGDB.org genome browser
If the results look correct, submit to MaizeGDB.org
uBLAST
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POPcorn: Project Portal for corn http://popcorn.maizegdb.org
CViT – Chromosome Viewing ToolDisplays features on chromosomes (linkage groups, pseudomolecules, chromosome arms, et cetera)
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POPcorn: Project Portal for corn http://popcorn.maizegdb.org
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