Sol2015 SGN Bioinformatics Tools
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The document discusses various bioinformatics tools available on the Sol Genomics Network (SGN) website. It describes SGN BLAST for searching nucleotide and protein sequences against plant genomes, the SGN VIGS Tool for designing virus-induced gene silencing constructs, JBrowse for visualizing genomic data tracks, and WebApollo for editing gene annotations. Other tools mentioned include the developing Tomato Expression Atlas and databases containing sequences from tomato and other plant species.
Sol2015 SGN Bioinformatics Tools
- 1. Sol Genomics Network SGN Workshop Bioinformatics Tools Noe Fernandez-Pozo Boyce Thompson Institute for Plant Research SOL Meeting 2015
- 2. Sol Genomics Network SGN Bioinformatics Tools New Tomato Expression Atlas in development WebApollo for tomato
- 3. Sol Genomics Network SGN BLAST https://solgenomics.net/tools/blast/
- 4. Sol Genomics Network SGN BLAST Input Database direct links Input auto detected Multi-FASTA analysis accepted Gene IDs and SGN Unigene IDs (eg: Solyc12g011330, SGN-U578092)
- 5. Sol Genomics Network SGN BLAST datasets Solanaceae species genomes, genes, and proteins: • Tomato • Potato • Pepper • Eggplant • N. benthamiana • N. tabacum TN90, K326 and BX Also: • Tomato wild species (S. pennellii and S. peruvianum) • Tomato inbred lines (BTI-87 and Gh13) • Other Nicotiana species (N. tometosiformis and N. sylvestris) • Markers • Coffee Genome • Organelles And more ... Petunia spp. Coming soon …
- 6. Sol Genomics Network BLAST Tabular Format
- 7. Sol Genomics Network Extracting sequences from BLAST databases
- 8. Sol Genomics Network Extracting sequences from BLAST databases
- 9. Sol Genomics Network SGNVIGS Tool http://vigs.solgenomics.net
- 10. Sol Genomics Network Virus-Induced Gene Silencing (VIGS) transformation mediated by A.tumefaciens or virus Ti Figure adapted from Azorsa et al. 2006 digested mRNA Azorsa D. et al. Gene silencing through RNA interference. (2006). Peptide Nucleic Acids, Morpholinos and Related Antisense Biomolecules. Editors: Janson C.G. and During M.J. pp 252-264 21-24 nt
- 11. Sol Genomics Network VIGS Tool input
- 12. Sol Genomics Network VIGS Tool output
- 13. Sol Genomics Network VIGS Tool output
- 14. Sol Genomics Network VIGS Tool output
- 15. Sol Genomics Network VIGS Tool output
- 16. Sol Genomics Network VIGS Tool output
- 17. Sol Genomics Network VIGS Tool output Target genes Off-Target genes Score Graph Predicted region Custom region
- 18. Sol Genomics Network 2 6 6 8 9 92 94 1315 2344 VIGS Tool Graph ExpandedView every siRNA mapped is shown
- 20. Sol Genomics Network SGN JBrowse https://solgenomics.net/jbrowse/
- 21. Sol Genomics Network SGN JBrowse
- 22. Sol Genomics Network SGN JBrowse gene models, markers, SNPs, RNA-Seq alignments, RNA-Seq coverage…
- 23. Sol Genomics Network SGN JBrowse gene models, markers, SNPs, RNA-Seq alignments, RNA-Seq coverage… Tomato genes linked to SGN on click Right click view details, highlight, zoom
- 24. Sol Genomics Network SGN JBrowse gene models, markers, SNPs, RNA-Seq alignments, RNA-Seq coverage…
- 25. Sol Genomics Network SGN JBrowse gene models, markers, SNPs, RNA-Seq alignments, RNA-Seq coverage…
- 26. Sol Genomics Network SGN JBrowse gene models, markers, SNPs, RNA-Seq alignments, RNA-Seq coverage… click on track: edit style, save data for region or whole track, GFF3, BED, Fasta
- 27. Sol Genomics Network SGN JBrowse Navigation, zoom in and out selecting a region
- 28. Sol Genomics Network SGN JBrowse Navigation, zoom in and out selecting a region find feature by name
- 29. Sol Genomics Network 360 Tomato variants
- 30. Sol Genomics Network 360 Tomato variants
- 31. Sol Genomics Network JBrowse: Nicotiana benthamiana bam files alignments and coverage Nicotiana benthamiana
- 32. Sol Genomics Network JBrowse: Nicotiana tabacum
- 33. Sol Genomics Network Tomato WebApollo http://tomato-webapollo.sgn.cornell.edu/WebApollo
- 34. Sol Genomics Network Tomato WebApollo
- 35. Sol Genomics Network Tomato WebApollo
- 36. Sol Genomics Network Tomato WebApollo
- 37. Sol Genomics Network Tomato WebApollo
- 38. Sol Genomics Network Tomato WebApollo
- 39. Sol Genomics Network Tomato WebApollo
- 40. Sol Genomics Network Tomato WebApollo
- 41. Sol Genomics Network Tomato WebApollo
- 42. Sol Genomics Network Tomato WebApollo
- 43. Sol Genomics Network Tomato WebApollo
- 45. Sol Genomics Network Jocelyn Rose Carmen Catala Jim Giovannoni Lukas A.Mueller Zhangjun Fei
- 46. Sol Genomics Network Computed Tomography images and videos
- 47. Sol Genomics Network Computed Tomography images and videos
- 48. Sol Genomics Network Tomato Expression Atlas
- 49. Sol Genomics Network Tomato Expression Atlas Laser dissection expression data Linked to SGN data
- 50. Sol Genomics Network Tomato Expression Atlas Laser dissection expression data Linked to SGN data
- 51. Thank you for your attention