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Bioinformatics Navigating the Web Accessible Data Plant Root Genomics Project MUPGRET Weekend Workshop Root Genomics Mini Conference Dr. Gordon K. Springer.

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Presentation on theme: "Bioinformatics Navigating the Web Accessible Data Plant Root Genomics Project MUPGRET Weekend Workshop Root Genomics Mini Conference Dr. Gordon K. Springer."— Presentation transcript:

1 Bioinformatics Navigating the Web Accessible Data Plant Root Genomics Project MUPGRET Weekend Workshop Root Genomics Mini Conference Dr. Gordon K. Springer February 20, 2005

2 MUPGRET-050220Bioinformatics2 tlcluster cluster over library tlcluster cluster over plate PHRED quality assessment ValSeq Validate Phred results & identify markers Crossmatch Eliminate vector Update Statistics for plate Update Statistics for library & project Plate available for annotation and database searching. Zip File Validation Trimming Keck to UMC EST Sequence Pipeline GBsubmit Prepare data for GB submission NCBI GenBank

3 MUPGRET-050220Bioinformatics3 Plant Root Genomics Home Direct Access http://genome.rnet.missouri.edu/Roots

4 MUPGRET-050220Bioinformatics4 Root Data Access

5 MUPGRET-050220Bioinformatics5 Getting Started from Menu

6 MUPGRET-050220Bioinformatics6 Project EST Statistics

7 MUPGRET-050220Bioinformatics7 Library Statistics

8 MUPGRET-050220Bioinformatics8 Look at a Plate of Data

9 MUPGRET-050220Bioinformatics9 Pick a Sequence

10 MUPGRET-050220Bioinformatics10 Looking at an EST Sequence

11 MUPGRET-050220Bioinformatics11 See Sequence in GenBank

12 MUPGRET-050220Bioinformatics12 Back to EST Sequence

13 MUPGRET-050220Bioinformatics13 See Similar Sequences at TIGR

14 MUPGRET-050220Bioinformatics14 Back to EST Sequence

15 MUPGRET-050220Bioinformatics15 Best Blast “Hits” in GenBank

16 MUPGRET-050220Bioinformatics16 Back to EST Sequence

17 MUPGRET-050220Bioinformatics17 Do a Blast Analysis

18 MUPGRET-050220Bioinformatics18 Blast Results from ZMRA

19 MUPGRET-050220Bioinformatics19 Clustering Data

20 MUPGRET-050220Bioinformatics20 Identifying Unigenes

21 MUPGRET-050220Bioinformatics21 Project Table

22 MUPGRET-050220Bioinformatics22 Live Demo http://genome.rnet.missouri.edu/Roots For Further Information: Rootgenomics Home Page Rootgenomics Home Page

23 MUPGRET-050220Bioinformatics23 Team Members Team Lead Gordon K. Springer * Post-doc William G. Spollen * IATS/RSC Larry Sanders Denis Hancock Mike Woodson Staff Hector Sanchez-Villeda * Steve Schroeder * UMC Graduate Students Chris Topinka Shafquat Bhuiyan Jay Hutchinson Abdul Khambati Rahul Patel Jim Ries * Arturo Guillen * http://beagle.rnet.missouri.edu/Biogroup * Root Project *Alumni

24 MUPGRET-050220Bioinformatics24 Stay Tuned The Story Continues … Questions?

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