Successfully reported this slideshow.
We use your LinkedIn profile and activity data to personalize ads and to show you more relevant ads. You can change your ad preferences anytime.

Vnti11 basics course

1,285 views

Published on

Published in: Technology, Business
  • Be the first to comment

Vnti11 basics course

  1. 1. basics course
  2. 2. Introduction <ul><li>Introduction </li></ul><ul><li>Database Explorer </li></ul><ul><li>Molecule Display </li></ul><ul><li>Molecule Editing </li></ul><ul><li>Restriction Enzymes </li></ul><ul><li>Primer Design and PCR analysis </li></ul><ul><li>Molecule construction (cloning) </li></ul>
  3. 3. Introduction <ul><li>Download VectorNTI11 from Invitrogen </li></ul><ul><li>http:// www.invitrogen.com /site/ us /en/home/ LINNEA-Online-Guides / LINNEA-Communities / Vector-NTI-Community / Vector-NTI.html </li></ul><ul><li>After installation the software will run in DEMO mode </li></ul><ul><li>until it is unlocked by a static or dynamic license. </li></ul><ul><li>Dynamic licenses are available by VIB (BITS). </li></ul>
  4. 4. Overview modules <ul><li>VectorNTI Explorer: </li></ul><ul><li>The database to store your data </li></ul><ul><li>VectorNTI: </li></ul><ul><li>Sequence creation, mapping, analysis, design, annotation, illustration and molecular biology data management </li></ul>
  5. 5. VectorNTI Explorer
  6. 6. VectorNTI Explorer
  7. 7. VectorNTI Explorer New Object
  8. 8. VectorNTI Explorer <ul><li>Organize your objects into groups using subsets </li></ul><ul><li>(and separators) </li></ul>New Subset
  9. 9. VectorNTI Explorer <ul><li>Organize your objects into groups using subsets </li></ul>separator Subset
  10. 10. VectorNTI Explorer New Object
  11. 11. VectorNTI Explorer New Object
  12. 12. VectorNTI Explorer New Object
  13. 13. VectorNTI Explorer New Object
  14. 14. VectorNTI Explorer New Object
  15. 15. VectorNTI Explorer
  16. 16. VectorNTI Explorer <ul><li>All molecules from all subsets are visible under MAIN </li></ul><ul><li>NEWMOL is in the MAIN set, not under any subset </li></ul>
  17. 17. VectorNTI Explorer <ul><li>All molecules from all subsets are visible under MAIN </li></ul><ul><li>NEWMOL is in the MAIN set, not under any subset </li></ul><ul><li>Place NEWMOL in a subset by clicking, holding and moving the name under MAIN to the subset name (DRAG and DROP) </li></ul>
  18. 18. VectorNTI Explorer <ul><li>Subsets and separators can be moved in a similar way </li></ul><ul><li>DELETE = delete from database </li></ul><ul><li>DISMISS = remove subset (molecules NOT removed) </li></ul><ul><li>CLEAR – EXCLUDE = remove molecules from subset, </li></ul><ul><li> NOT from MAIN database </li></ul>
  19. 19. VectorNTI Explorer <ul><li>Subsets and separators can be moved in a similar way </li></ul><ul><li>DELETE = delete from database (= pressing ‘delete’!) </li></ul><ul><li>DISMISS = remove subset (molecules NOT removed) </li></ul><ul><li>CLEAR – EXCLUDE = remove molecules from subset, </li></ul><ul><li> NOT from MAIN database </li></ul>
  20. 20. VectorNTI Explorer <ul><li>Subsets and separators can be moved in a similar way </li></ul><ul><li>DELETE = delete from database </li></ul><ul><li>DISMISS = remove subset (molecules NOT removed) </li></ul><ul><li>CLEAR – EXCLUDE = remove molecules from subset, </li></ul><ul><li> NOT from MAIN database </li></ul>
  21. 21. VectorNTI Explorer subset selected molecule selected
  22. 22. VectorNTI Explorer
  23. 23. VectorNTI Explorer
  24. 24. VectorNTI Explorer We want to gather all NCBI molecules in a separate subset for easy access
  25. 25. VectorNTI Explorer
  26. 26. VectorNTI Explorer
  27. 27. VectorNTI Explorer
  28. 28. VectorNTI Explorer
  29. 29. VectorNTI Explorer
  30. 30. VectorNTI Explorer
  31. 31. VectorNTI Explorer
  32. 32. VectorNTI Explorer
  33. 33. VectorNTI Explorer Backup on other location e.g. network drive or external drive Local database on network drive » use same database on ≠ computers We want to add some more structured information to each entry -> new field!
  34. 34. VectorNTI Explorer New field Import fields
  35. 35. VectorNTI Explorer
  36. 36. VectorNTI Explorer
  37. 37. VectorNTI Explorer
  38. 38. VectorNTI Explorer
  39. 39. VectorNTI Explorer
  40. 40. VectorNTI Explorer
  41. 41. VectorNTI Explorer Paste the data in e.g. Excel
  42. 42. VectorNTI Explorer <ul><li>Summary </li></ul><ul><li>» Create, edit and delete objects and subsets </li></ul><ul><li>» Organize objects into convenient groups (subsets) </li></ul><ul><li>» Import and export objects and archives </li></ul><ul><li>» Perform database searches </li></ul>
  43. 43. VectorNTI Explorer <ul><li>Exercises </li></ul><ul><li>» Import restriction enzymes from REBASE </li></ul><ul><li> http:// rebase.neb.com (bairoch.nnn file) </li></ul><ul><li>» Add a new DNA marker </li></ul><ul><li> in the Gel Markers database </li></ul><ul><li>» Select the pUC plasmids and export them </li></ul><ul><li> into an archive file </li></ul><ul><li>» Make 2 RE subsets: </li></ul><ul><li> (1) BamHI, EcoRI, EcoRV, HindIII, NcoI, </li></ul><ul><li> NdeI, PstI, PvuI, SmaI and XmaI </li></ul><ul><li> (2) 6bp non-ambiguous </li></ul>
  44. 44. VectorNTI Explorer http://Rebase.neb.com/rebase/rebase.html
  45. 45. VectorNTI Explorer
  46. 46. VectorNTI Explorer Save file as... » bairoch.nnn R
  47. 47. VectorNTI Explorer <ul><li>Exercises </li></ul><ul><li>» Import restriction enzymes from REBASE </li></ul><ul><li> http:// rebase.neb.com (bairoch.nnn file) </li></ul><ul><li>» Add a new DNA marker </li></ul><ul><li> in the Gel Markers database </li></ul><ul><li>» Select the pUC plasmids and export them </li></ul><ul><li> into an archive file </li></ul><ul><li>» Make 2 RE subsets: </li></ul><ul><li> (1) BamHI, EcoRI, EcoRV, HindIII, NcoI, </li></ul><ul><li> NdeI, PstI, PvuI, SmaI and XmaI </li></ul><ul><li> (2) 6bp non-ambiguous </li></ul>
  48. 48. VectorNTI <ul><li>Start VectorNTI... </li></ul>
  49. 49. VectorNTI <ul><li>... </li></ul>MAIN MENU Links to the other modules of the Vector NTI suite
  50. 50. VectorNTI <ul><li>... </li></ul>MAIN TOOLBAR Changeable toolbar Depending on which pane is active
  51. 51. VectorNTI <ul><li>... </li></ul>TEXT WINDOW
  52. 52. VectorNTI <ul><li>... </li></ul>GRAPHICS WINDOW
  53. 53. VectorNTI <ul><li>... </li></ul>SEQUENCE WINDOW
  54. 54. VectorNTI <ul><li>... </li></ul>Local Database
  55. 55. VectorNTI <ul><li>... </li></ul>Open the local database
  56. 56. VectorNTI <ul><li>... </li></ul>Click pACYC177 to open
  57. 57. VectorNTI <ul><li>... </li></ul>Resize windows for a better view
  58. 58. VectorNTI <ul><li>... </li></ul>
  59. 59. VectorNTI <ul><li>... </li></ul>
  60. 60. VectorNTI <ul><li>... </li></ul>
  61. 61. VectorNTI <ul><li>... </li></ul>
  62. 62. VectorNTI <ul><li>... </li></ul>Copy complete graphics 1
  63. 63. VectorNTI <ul><li>... </li></ul>
  64. 64. VectorNTI <ul><li>... </li></ul>
  65. 65. VectorNTI <ul><li>... </li></ul>
  66. 66. VectorNTI <ul><li>... </li></ul>
  67. 67. VectorNTI <ul><li>... </li></ul>but COPY (Ctrl+C) & PASTE (Ctrl+V) also works...
  68. 68. VectorNTI <ul><li>... </li></ul>
  69. 69. VectorNTI <ul><li>... </li></ul>
  70. 70. VectorNTI <ul><li>... </li></ul>
  71. 71. VectorNTI <ul><li>... </li></ul>
  72. 72. VectorNTI <ul><li>... </li></ul>
  73. 73. VectorNTI <ul><li>... </li></ul>
  74. 74. VectorNTI <ul><li>... </li></ul>
  75. 75. VectorNTI <ul><li>... </li></ul>
  76. 76. VectorNTI <ul><li>... </li></ul>Open the local database
  77. 77. VectorNTI <ul><li>... </li></ul>Click pBR322 to open
  78. 78. VectorNTI <ul><li>... </li></ul>
  79. 79. VectorNTI <ul><li>... </li></ul>Molecule display setup
  80. 80. VectorNTI <ul><li>... </li></ul>
  81. 81. VectorNTI <ul><li>... </li></ul>
  82. 82. VectorNTI <ul><li>... </li></ul>
  83. 83. VectorNTI <ul><li>... </li></ul>
  84. 84. VectorNTI <ul><li>... </li></ul>
  85. 85. VectorNTI <ul><li>... </li></ul>
  86. 86. VectorNTI <ul><li>... </li></ul>
  87. 87. VectorNTI <ul><li>... </li></ul>
  88. 88. VectorNTI <ul><li>... </li></ul>
  89. 89. VectorNTI <ul><li>... </li></ul>
  90. 90. VectorNTI <ul><li>... </li></ul>How to edit your molecule
  91. 91. VectorNTI <ul><li>... </li></ul>
  92. 92. VectorNTI <ul><li>... </li></ul>
  93. 93. VectorNTI <ul><li>... </li></ul>
  94. 94. VectorNTI <ul><li>... </li></ul>
  95. 95. VectorNTI <ul><li>... </li></ul>
  96. 96. VectorNTI <ul><li>... </li></ul>
  97. 97. VectorNTI <ul><li>... </li></ul>
  98. 98. VectorNTI <ul><li>... </li></ul>
  99. 99. VectorNTI <ul><li>... </li></ul>
  100. 100. VectorNTI <ul><li>... </li></ul>
  101. 101. VectorNTI <ul><li>... </li></ul>
  102. 102. VectorNTI <ul><li>... </li></ul>
  103. 103. VectorNTI <ul><li>... </li></ul>
  104. 104. VectorNTI <ul><li>... </li></ul>
  105. 105. VectorNTI <ul><li>... </li></ul>Link Panes
  106. 106. VectorNTI <ul><li>... </li></ul>
  107. 107. VectorNTI <ul><li>... </li></ul>
  108. 108. VectorNTI <ul><li>... </li></ul>
  109. 109. VectorNTI <ul><li>... </li></ul>
  110. 110. VectorNTI <ul><li>... </li></ul>
  111. 111. VectorNTI <ul><li>... </li></ul>
  112. 112. VectorNTI <ul><li>... </li></ul>
  113. 113. VectorNTI <ul><li>... </li></ul>
  114. 114. VectorNTI <ul><li>... </li></ul>
  115. 115. VectorNTI <ul><li>... </li></ul>
  116. 116. VectorNTI <ul><li>... </li></ul>
  117. 117. VectorNTI <ul><li>... </li></ul>
  118. 118. VectorNTI: Molecule Editing <ul><li>Close My pBR322 </li></ul><ul><li>Formatting the graphics of a molecule: </li></ul><ul><li>» NCBI nucleotide database: NM_001025366 </li></ul>
  119. 119. VectorNTI: Molecule Editing <ul><li>... </li></ul>Retrieve directly from NCBI into VectorNTI: » Tools » Open » Retrieve... NM_001025366
  120. 120. VectorNTI: Molecule Editing <ul><li>... </li></ul>
  121. 121. VectorNTI: Molecule Editing <ul><li>... </li></ul>
  122. 122. VectorNTI: Molecule Editing <ul><li>... </li></ul>
  123. 123. VectorNTI: Molecule Editing <ul><li>... </li></ul>
  124. 124. VectorNTI: Molecule Editing <ul><li>... </li></ul>
  125. 125. VectorNTI: Molecule Editing <ul><li>... </li></ul>Ctrl + click » ARRANGEMENT
  126. 126. VectorNTI: Molecule Editing <ul><li>... </li></ul>Graphics Display Setup >> all features will be displayed in their specific way
  127. 127. VectorNTI: Molecule Editing <ul><li>... </li></ul>Feature Display Setup >> change the way this feature is displayed
  128. 128. VectorNTI: Molecule Editing <ul><li>... </li></ul>
  129. 129. VectorNTI: Molecule Editing <ul><li>... </li></ul>Picture Editing Mode
  130. 130. VectorNTI: Molecule Editing <ul><li>... </li></ul>
  131. 131. VectorNTI: Molecule Editing <ul><li>Molecule display setup: </li></ul><ul><li> » deselect restriction map to hide the RE sites </li></ul><ul><li>Graphics display setup: new style for CDS feature </li></ul><ul><li>» Shape 0 + More... (fill color + darker color for border) </li></ul><ul><li>Save the molecule in the database </li></ul>
  132. 132. VectorNTI: Molecule Editing <ul><li>... </li></ul>Change graphical display
  133. 133. VectorNTI: Molecule Editing <ul><li>... </li></ul>
  134. 134. VectorNTI: Molecule Editing <ul><li>... </li></ul>
  135. 135. VectorNTI: Molecule Editing <ul><li>... </li></ul>
  136. 136. VectorNTI: Molecule Editing <ul><li>... </li></ul>
  137. 137. VectorNTI: Molecule Editing <ul><li>... </li></ul>
  138. 138. VectorNTI: Molecule Editing <ul><li>... </li></ul>
  139. 139. VectorNTI: Molecule Editing <ul><li>... </li></ul>
  140. 140. VectorNTI: Molecule Editing <ul><li>... </li></ul>
  141. 141. VectorNTI: Molecule Editing <ul><li>... </li></ul>
  142. 142. VectorNTI: Molecule Editing <ul><li>... </li></ul>
  143. 143. VectorNTI: Molecule Editing <ul><li>... </li></ul>
  144. 144. VectorNTI: Molecule Editing <ul><li>... </li></ul>
  145. 145. VectorNTI: Restriction enzymes <ul><li>... </li></ul>
  146. 146. VectorNTI: Restriction enzymes <ul><li>Import enzymes </li></ul><ul><li>» From archive » DBINIT.EA4 </li></ul><ul><li>» From REBASE » baroich.nnn </li></ul><ul><li>Restriction map setup </li></ul><ul><li>Restriction analysis and report </li></ul><ul><li>Restriction digestion and gel display </li></ul><ul><li>Open pUC19 from the database </li></ul>
  147. 147. VectorNTI: Restriction enzymes <ul><li>... </li></ul>
  148. 148. VectorNTI: Restriction enzymes <ul><li>... </li></ul>
  149. 149. VectorNTI: Restriction enzymes <ul><li>... </li></ul>
  150. 150. Primer design and PCR analysis <ul><li>... </li></ul>
  151. 151. Primer design and PCR analysis <ul><li>... </li></ul>
  152. 152. Primer design and PCR analysis <ul><li>... </li></ul>
  153. 153. Primer design and PCR analysis <ul><li>... </li></ul>Select 2 enzymes (use Ctrl) e.g. PvuI and EcoRV
  154. 154. Molecule construction (cloning) <ul><li>... </li></ul>
  155. 155. Molecule construction (cloning) <ul><li>... </li></ul>
  156. 156. Molecule construction (cloning) <ul><li>... </li></ul>Restriction Analysis and Report
  157. 157. Molecule construction (cloning) <ul><li>... </li></ul>
  158. 158. Molecule construction (cloning) <ul><li>... </li></ul>
  159. 159. Molecule construction (cloning) <ul><li>... </li></ul>
  160. 160. Molecule construction (cloning) <ul><li>... </li></ul>
  161. 161. Molecule construction (cloning) <ul><li>... </li></ul>
  162. 162. Molecule construction (cloning) <ul><li>... </li></ul>
  163. 163. Molecule construction (cloning) <ul><li>... </li></ul>
  164. 164. Molecule construction (cloning) <ul><li>... </li></ul>Select BamHI and PvuI
  165. 165. Molecule construction (cloning) <ul><li>... </li></ul>
  166. 166. Molecule construction (cloning) <ul><li>... </li></ul>
  167. 167. VectorNTI: Restriction enzymes <ul><li>... </li></ul>
  168. 168. VectorNTI: Restriction enzymes <ul><li>... </li></ul>
  169. 169. VectorNTI: Restriction enzymes <ul><li>... </li></ul>
  170. 170. VectorNTI: Restriction enzymes <ul><li>... </li></ul>
  171. 171. VectorNTI: Restriction enzymes <ul><li>... </li></ul>
  172. 172. VectorNTI: Restriction enzymes <ul><li>... </li></ul>
  173. 173. VectorNTI: Restriction enzymes <ul><li>... </li></ul>
  174. 174. Primer design and PCR analysis <ul><li>Primer design for PCR on GST from plasmid pGEX-5G/LIC </li></ul><ul><li>GST: 258-935 bp | MCS: BamHI (951), Xma (956), EcoRI (961) </li></ul><ul><li>Molecule construction: GST in pET104-DEST (NdeI – XmaI) </li></ul>
  175. 175. Primer design and PCR analysis <ul><li>... </li></ul>
  176. 176. Primer design and PCR analysis <ul><li>... </li></ul>
  177. 177. Primer design and PCR analysis <ul><li>... </li></ul>
  178. 178. Primer design and PCR analysis <ul><li>... </li></ul>
  179. 179. Primer design and PCR analysis <ul><li>... </li></ul>
  180. 180. Primer design and PCR analysis <ul><li>... </li></ul>
  181. 181. Primer design and PCR analysis <ul><li>... </li></ul>
  182. 182. Primer design and PCR analysis <ul><li>... </li></ul>
  183. 183. Primer design and PCR analysis <ul><li>... </li></ul>
  184. 184. Primer design and PCR analysis <ul><li>... </li></ul>
  185. 185. Primer design and PCR analysis <ul><li>... </li></ul>
  186. 186. Primer design and PCR analysis <ul><li>... </li></ul>
  187. 187. Primer design and PCR analysis <ul><li>... </li></ul>
  188. 188. Primer design and PCR analysis <ul><li>... </li></ul>
  189. 189. Primer design and PCR analysis <ul><li>... </li></ul>
  190. 190. Primer design and PCR analysis <ul><li>... </li></ul>
  191. 191. Primer design and PCR analysis <ul><li>... </li></ul>
  192. 192. Primer design and PCR analysis <ul><li>... </li></ul>
  193. 193. Primer design and PCR analysis <ul><li>... </li></ul>
  194. 194. Primer design and PCR analysis <ul><li>... </li></ul>
  195. 195. Primer design and PCR analysis <ul><li>... </li></ul>
  196. 196. Primer design and PCR analysis <ul><li>... </li></ul>
  197. 197. Primer design and PCR analysis <ul><li>... </li></ul>
  198. 198. Primer design and PCR analysis <ul><li>... </li></ul>
  199. 199. Primer design and PCR analysis <ul><li>... </li></ul>
  200. 200. Primer design and PCR analysis <ul><li>... </li></ul>
  201. 201. Primer design and PCR analysis <ul><li>... </li></ul>
  202. 202. Molecule construction (cloning) <ul><li>With the Fragment Wizard you can construct </li></ul><ul><li>a new DNA molecule </li></ul><ul><li>Define the needed fragments for the </li></ul><ul><li>Goal Molecule Definition list </li></ul><ul><li>Molecule construction: </li></ul><ul><li>cloning GST in pET104-DEST (NdeI – XmaI) </li></ul>
  203. 203. Primer design and PCR analysis <ul><li>... </li></ul>
  204. 204. Molecule construction (cloning) <ul><li>... </li></ul>
  205. 205. Molecule construction (cloning) <ul><li>... </li></ul>
  206. 206. Molecule construction (cloning) <ul><li>... </li></ul>
  207. 207. Molecule construction (cloning) <ul><li>... </li></ul>
  208. 208. Molecule construction (cloning) <ul><li>... </li></ul>
  209. 209. Molecule construction (cloning) <ul><li>... </li></ul>
  210. 210. Molecule construction (cloning) <ul><li>... </li></ul>hold shift key and click in RE! else Fragment wizard reverts to 5’!
  211. 211. Molecule construction (cloning) <ul><li>... </li></ul>
  212. 212. Molecule construction (cloning) <ul><li>... </li></ul>
  213. 213. Molecule construction (cloning) <ul><li>... </li></ul>
  214. 214. Molecule construction (cloning) <ul><li>... </li></ul>
  215. 215. Molecule construction (cloning) <ul><li>... </li></ul>
  216. 216. Molecule construction (cloning) <ul><li>... </li></ul>
  217. 217. Molecule construction (cloning) <ul><li>... </li></ul>
  218. 218. Molecule construction (cloning) <ul><li>... </li></ul>
  219. 219. Molecule construction (cloning) <ul><li>... </li></ul>
  220. 220. Molecule construction (cloning) <ul><li>... </li></ul>
  221. 221. Molecule construction (cloning) <ul><li>... </li></ul>hold shift key and click in RE! else Fragment wizard reverts to 5’!
  222. 222. Molecule construction (cloning) <ul><li>... </li></ul>
  223. 223. Molecule construction (cloning) <ul><li>... </li></ul>
  224. 224. Molecule construction (cloning) <ul><li>... </li></ul>
  225. 225. Molecule construction (cloning) <ul><li>... </li></ul>
  226. 226. Molecule construction (cloning) <ul><li>... </li></ul>
  227. 227. Molecule construction (cloning) <ul><li>... </li></ul>
  228. 228. Molecule construction (cloning) <ul><li>... </li></ul>
  229. 229. Molecule construction (cloning) <ul><li>... </li></ul>
  230. 230. Molecule construction (cloning) <ul><li>Exercises </li></ul><ul><li>» Amplify the SV40 promoter from plasmid pRSVneo </li></ul><ul><li> Add a HindIII site to the 5’ end </li></ul><ul><li>and a SmaI site to the 3’ end </li></ul><ul><li> Save the result as SV40prom </li></ul><ul><li>» Clone the SV40 promoter using the </li></ul><ul><li> HindIII-SmaI in pUC18 </li></ul><ul><li> Save as pUC18-SV40 </li></ul>

×