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Tour of BioBIKE Motif Discovery. BioBIKE (Biological Integrated Knowledge Environment) combines: Knowledge: All known genomes of interest to a specific scientific community.

Patman
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  1. Tour of BioBIKEMotif Discovery BioBIKE (Biological Integrated Knowledge Environment) combines: Knowledge:All known genomes of interest to a specific scientific community. Analytical Tools: A powerful graphical language that permits creative expression to those with no programming experience Various BioBIKEs are available through: http://biobike.csbc.vcu.edu This demonstration is best viewed as a slide show,enabling you to simulate a session and make changes in cursor position more obvious.To do this, click Slide Show on the top tool bar, then View show. Click anywhere to go on to the next slide

  2. Tour of BioBIKEMotif Discovery In this tour, you'll see how to: Slide 4 13,19 16 31 48 53 • Log onto CyanoBIKE • Find a gene from a short description of it • Speak BioBIKE (the language of CyanoBIKE) • Find orthologs of a gene • Obtain upstream sequences of a gene or list of genes • Search a set of sequences for common motifs You can go to any slide in this tour at any time by typing the slide number and pressing Enter. Or go to the next slide by clicking the mouse.

  3. Coming Attractions! If you like this tour, you might also try: Sequence Analysis • Display a sequence • Find similar sequences amongst metagenomes, known viruses, everything in GenBank • Make a sequence alignment from a set of similar sequences • Construct a phylogenetic tree Analysis of Metagenome Aggregates • Find the number of contigs in a metagenome • Find the average contig size in a metagenome • Find the average GC content within a metagenome • Visualize the distribution of GC content amongst the contigs of a metagenome

  4. To get to CyanoBIKE, click a link to one of the public sites/ To see more tours like this one, click Guided tours of BioBIKE Access this site at htpp://biobike.csbc.vcu.edu

  5. Your name (no spaces) - Enter anything you like as a login name, but no spaces or symbols.- EMail address is optional but may be useful if you want to send in questions or complaints.- Click New Login

  6. Function palette Workspace The BioBIKE environment is divided into three areas as shown. You'll bring functions down from the function palette to the workspace, execute them, and note the results in the results window Results window

  7. HELP! PROBLEM Two very important buttons on the function palette: On-line help (general) Something went wrong? Tell us!

  8. Two very important buttons in the workspace: Undo (return to workspace before last action) Redo (Get back the workspace you undid)

  9. Our Story The glnA gene in the cyanobacterium Anabaena PCC 7120 encodes glutamine synthetase, a critical enzyme in nitrogen metabolism. The transcription of this gene is regulated by the availability of a nitrogen source. Suppose you want to understand the molecular mechanism by which the regulation takes place.

  10. Our Story Your strategy is to presume that this highly conserved gene possesses the same upstream regulatory sequences in related organisms. You will collect orthologs of glnA in related organisms, collect their upstream sequences, and examine them for a conserved sequence motif. The first step is to get in hand oneglnA gene, the one you already know about in Anabaena. Mouse over the GENES-PROTEINS button.

  11. Mousing over a button in the function pallette causes a menu to appear. You know the unofficial name of the gene, "glnA", and from that you want to get the official name of the gene described by "glnA". Mouse over DESCRIPTION-ANALYSIS.

  12. Click on the function GENE-DESCRIBED-BY.

  13. A GENE-DESCRIBED-BY function box is now in the workspace. Before continuing with the problem, let's consider what function boxes mean.

  14. Argument(object) Function-name Flag Keyword object General Syntax of BioBIKE The basic unit of BioBIKE is the function box. It consists of the name of a function, perhaps one or more required arguments, and optional keywords and flags. A function may be thought of as a black box: you feed it information, it produces a product.

  15. Argument(object) Function-name Flag Keyword object General Syntax of BioBIKE Function boxes contain the following elements: • Function-name (e.g. SEQUENCE-OF or LENGTH-OF) • Argument: Required, acted on by function • Keyword clause: Optional, more information • Flag: Optional, more (yes/no) information

  16. Argument(object) Function-name Flag Keyword object • Option icon: Brings up a menu of keywords and flags • Action icon: Brings up a menu enabling you to execute a function, copy and paste, information, get help, etc • Clear/Delete icon: Removes information you entered or removes box entirely General Syntax of BioBIKE … and icons to help you work with functions:

  17. Back to our story. Click on the Argument box to open it for entry…

  18. …then type in the description you know, "glnA".

  19. A very common error is to forget to close an entry box. A function can't be executed until all entry boxes are closed, either by pressing Enter or Tab. Do one or the other.

  20. Left to it's own devices, BioBIKE will search every organism it knows about for genes described by "glnA". You'll get a much faster response if you modify the function to search only Anabaena. Do this by mousing over the Option Icon…

  21. … and clicking the IN option.

  22. Then open the IN object box for entry by clicking on it.

  23. You could type in the official name or nickname of the organism, but if you don't happen to know it, find it by mousing over the DATA button…

  24. Anabaena PCC 7120 is a nitrogen-fixing cyanobacterium. Mouse over that choice.

  25. Mouse over Anabaena PCC 7120,…

  26. … and click on its official nickname, A7120.

  27. That causes the name to appear in the selected box. The function is now ready for execution. Mouse over the Action Icon…

  28. … and click Execute.

  29. A result now appears in the Result Window. With the name of the gene in hand, you want to find all orthologs of it in cyanobacteria, to extract their upstream sequences. Mouse over the GENES-PROTEINS button…

  30. … and click ORTHOLOG-OF.

  31. Open the argument box of the function for entry by clicking on it…

  32. And type in the nickname of Anabaena's glnA gene, alr2328.

  33. Close the entry box by pressing Enter or Tab…

  34. … and execute the function.

  35. Lots of orthologs! It would be helpful to be able to refer to them as a group. To define such a group, mouse over the DEFINITION button…

  36. … and click the DEFINE function.

  37. The DEFINE function asks for two things: the name of the variable to be defined and the value it is to be given. The value will be all those orthologs. The name is up to you. Click on the variable argument box to open it up for entry…

  38. … and type a name that makes sense to you, closing the box afterwards by pressing Tab.

  39. Tab closes the entry box and automatically opens the next one (if it exists). There are many ways of getting that list of orthologs. You could copy and paste that list from the Result pane to the open value box, but it might be more clear to cut/paste the function that produced it. Let me show you. Click on the Action icon of ORTHOLOG-OF.

  40. Click Cut. The function box will disappear but will be retained in the BioBIKE clipboard.

  41. … then mouse over the Action Icon of the value argument box…

  42. … and click Paste.

  43. The definition is now complete (and reads well for future reference). But it will not take effect until the function is executed Click the Action icon.

  44. … and click Execute.

  45. Notice that a new VARIABLES button appears. We'll use it later to access the newly defined list. For now, we need to get upstream regions from all those genes. Mouse over the GENES-PROTEINS button…

  46. … then mouse over GENES-NEIGHBORHOOD…

  47. … and click the SEQUENCE-UPSTREAM-OF function.

  48. The function seems to call for a gene as the argument. However, like most BioBIKE functions, this one has the following useful property: - Give it a single item, it returns a single answer - Give it a list of items, it returns a list of answers. Open the argument box for input.

  49. We want the function to act on the group of genes we just defined. Mouse over the VARIABLES button…

  50. … and click the name of the group you just defined. That will bring the group into the selected box.

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