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POPcorn : P roject P ortal for corn http://popcorn.maizegdb.org

POPcorn : P r o ject P ortal for corn A set of project and sequence-indexed data searching resources (http://popcorn.maizegdb.org) Jack M. Gardiner Poster P897. A set of project and sequence-indexed data searching resources. POPcorn : P roject P ortal for corn http://popcorn.maizegdb.org.

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POPcorn : P roject P ortal for corn http://popcorn.maizegdb.org

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  1. POPcorn: ProjectPortal for cornA set of project and sequence-indexed data searching resources(http://popcorn.maizegdb.org)Jack M. GardinerPoster P897

  2. A set of project and sequence-indexed data searching resources POPcorn: Project Portal for corn http://popcorn.maizegdb.org http://popcorn.maizegdb.org

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

  4. POPcorn: Project Portal for corn http://popcorn.maizegdb.org • Project Objectives: • Difficult to find all online resources relevant to one’s research • Project Search

  5. POPcorn: Project Portal for corn www.maizegdb.org/POPcorn • Project Objectives: • Difficult to find all online resources relevant to one’s research • Project Search • Repeated BLAST searches at multiple sites • POPcorn BLAST

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

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

  8. POPcorn: Project Portal for corn http://popcorn.maizegdb.org • Project Search • Database of maize research projects and online resources • Hand-curated and updated monthly; 97 projects, 128 resources

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

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

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

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

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

  14. POPcorn: Project Portal for corn http://popcorn.maizegdb.org • Two options for searching with a sequence • Simple sequence to sequence search (BLAST) • Sequenced index search (access biological resources associated with a sequence)

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

  16. POPcorn: Project Portal for corn http://popcorn.maizegdb.org • BLAST against target sequence at multiple websites using Web Services • Results can be returned via email

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

  18. Sequence-indexed data search • Carries out complex searches • One or more searches at once POPcorn: Project Portal for corn http://popcorn.maizegdb.org

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

  20. POPcorn: Project Portal for corn http://popcorn.maizegdb.org • An example: steps taken to find a UniformMu stock containing a given mutation. • BLAST query sequence against NCBI GSS • Parse definition line to get UniformMu locus name • Get LOCUS record at MaizeGDB • Get VARIATION record(s) for that LOCUS at MaizeGDB • Get UniformMu STOCK records for each VARIATION at MaizeGDB • Construct links to MGC Stock Center for each stock found.

  21. POPcorn: Project Portal for corn http://popcorn.maizegdb.org • An example: steps taken to find a UniformMu stock containing a given mutation. • BLAST query sequence against NCBI GSS • Parse definition line to get UniformMu locus name • Get LOCUS record at MaizeGDB • Get VARIATION records for that LOCUS at MaizeGDB • Get UniformMu STOCK records for each VARIATION at MaizeGDB • Construct links to MGC Stock Center for each stock found.

  22. POPcorn: Project Portal for corn http://popcorn.maizegdb.org uBLAST Select a target database Input your sequence (split files larger than 20MB) Provide some information about your data Submit! 22

  23. POPcorn: Project Portal for corn http://popcorn.maizegdb.org uBLAST Monitor progress of your job 23 You will receive an e-mail when your job is complete

  24. POPcorn: Project Portal for corn http://popcorn.maizegdb.org uBLAST Check your alignment on the MaizeGDB.org genome browser If the results look correct, submit to MaizeGDB.org 24

  25. POPcorn: Project Portal for corn http://popcorn.maizegdb.org CViT – ChromosomeViewingTool Displays features on chromosomes (linkage groups, pseudomolecules, chromosome arms, et cetera) 25

  26. POPcorn: Project Portal for corn http://popcorn.maizegdb.org CViT – ChromosomeViewingTool 26

  27. MaizeGDB/POPcorn team POPcorn Principal 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) Poster P897

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