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Accessing Sequence Resources

Authors:

David M. Francis, The Ohio State University; Heather L. Merk, The Ohio State University

These webinars and the accompanying pdf (at the bottom of the page) were presented at the 2010 Tomato Disease Workshop. The videos provide overviews of available genome sequence resources for tomato, including NCBI, SWISS-PROT, EMBL, SGN, SolCAP, and the Gene Index Project. The final video provides an introduction to customized searches using the ENTREZ tool on NCBI.

In this video, Dr. David Francis, The Ohio State University, provides an overview of available genome sequence resources for tomato, including National Center for Biotechnology Information (NCBI), UniProt (SWISS-PROT), European Molecular Biology Laboratory (EMBL), Solanaceae Genomics Network (SGN), Solanaceae Coordinated Agricultural Project (SolCAP), and The Gene Index Project, formerly at TIGR and now housed at Harvard University.

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In this video, Dr. Francis provides an overview of information housed at the NCBI. First, Dr. Francis reviews available information in GenBank’s nucleotide database, including detailed annotation of gene features, translated nucleotide sequence into amino acid sequence, and the nucleotide sequence in FASTA format. Second, Dr. Francis highlights information contained in four sequence databases at NCBI: the nucleotide database, the EST (Expressed Sequence Tag) database, the GSS (Genomic Short Sequence) database, and the UniGene database.

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In this video, Dr. Francis provides an overview of the SWISS-PROT (UniProt) database, which contains high quality annotation. In addition, information is non-redundant and cross-referenced with other databases.

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In this video, Dr. Francis provides an overview of genomics tools available at the Arabidopsis Information Resource (TAIR).

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In this video, Dr. Francis provides an introduction to the Gene Indices housed at Harvard University’s Computational Biology and Functional Genomics Laboratory.

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In this video, Dr. Francis provides an overview of the tomato genome data available at the Solanaceae Genome Network (SGN). In addition, Dr. Francis describes the transcriptome sequence of tomato varieties that SolCAP has developed.

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In this video, Dr. Francis provides an overview of resources developed by SolCAP. The resources for tomato include germplasm information, genotypic data, and phenotypic data. SolCAP has also developed searchable SNP datasets.

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In this video, Dr. Francis provides an introduction to the ENTREZ tool for the NCBI database. He demonstrates how to use ENTREZ searches to acquire subsets of data that can be used in marker discovery. Dr. Francis performs sample searches to help users learn how to optimize database searches.

If you experience problems viewing this video connect directly to our YouTube channnel or see the YouTube troubleshooting guide.

Find all the presentations from the 2010 Tomato Disease Workshop

External Links

  • EMBL Nucleotide Sequence Database [Online]. European Bioinformatics Institute, European Molecular Biology Laboratory. Available at: http://www.ebi.ac.uk/embl/ (verified 4 Jan 2011).
  • National Center for Biotechnology Information [Online]. U.S. National Library of Medicine, National Institutes of Health. Available at: http://www.ncbi.nlm.nih.gov/ (verified 4 Jan 2011).
  • Sol Genomics Network [Online]. Available at: http://solgenomics.net/ (verified 4 Jan 2011).
  • Solanaceae Coordinated Agricultural Project [Online]. Michigan State University. Available at: http://solcap.msu.edu/ (verified 4 Jan 2011).
  • The Arabidopsis Information Resource [Online]. Available at: http://www.arabidopsis.org/ (verified 4 Jan 2011).
  • The Gene Index Project [Online]. Computational Biology and Functional Genomics Laboratory, Harvard University. Available at: http://compbio.dfci.harvard.edu/tgi/ (verified 4 Jan 2011).
  • UniProt [Online]. Available at: http://www.uniprot.org/ (verified 4 Jan 2011).

Funding Statement

Development of this lesson was supported in part by the National Institute of Food and Agriculture (NIFA) Solanaceae Coordinated Agricultural Project, agreement 2009-85606-05673, administered by Michigan State University. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the United States Department of Agriculture.

Attachments:

Sequence_Resources.pdf (4.08 MB)

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