1. Idealized example of FOR-EACH Loop and IF
Scientific objective
Identify upstream regions with protein-binding site
TGC CAT
in Anabaena PCC 7120
Upstream region A T
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. Click at any time Click to clear screen
Problem calls for a loop. (Click on menu)
Undo | Redo
Workspace
Find functions in categories shown above
Click for menu of box operations
Function-specific options
Deletes box
Function box
ORTHOLOG-OF
gene-or-protein IN |
CUTOFF
1e-10
Click on box to select (red outline) input box
Click to extend function for menu of options
Potential input box + type of needed input
Clears box
Click at any time
Click to clear screen
Results

3. Click at any time Click to clear screen
FOR-EACH is a version of LOOP that may be more readable for some. (Click on arrow)
Logical comparison
Logical connectives
Loops and conditional executions Other logic functions
BOTH
EITHER
FOR-EACH IF
IF-NOT
LOOP
NOT
ORDER
Undo | Redo
Workspace
Find functions in categories shown above
Click for menu of box operations
Function-specific options
Deletes box
Function box
ORTHOLOG-OF
gene-or-protein IN |
CUTOFF
1e-10
Click on box to select (red outline) input box
Click to extend function for menu of options
Potential input box + type of needed input
Clears box
Click at any time
Click to clear screen
Results

4. Undo | Redo
Workspace
First step is to name the variable that will be iterated during the loop. Any name will do.
FOR-EACH
variable name
Control section – Determines form of iteration
Initialization section – Initializes loop variables before the loop begins
Variable update section – Resets loop variables each iteration
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

5. Click on green arrow for choices of type of iteraation.
Undo | Redo
Workspace
Click on green arrow for choices of type of iteraation.
FOR-EACH
gene|
Control section – Determines form of iteration
Initialization section – Initializes loop variables before the loop begins
Variable update section – Resets loop variables each iteration
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

6. Control section – Determines form of iteration
Undo | Redo
Workspace
FOR-EACH
gene
IN list
FROM number
FROM number BY number
FROM number TO number
FROM number TO number BY number
Control section – Determines form of iteration
Initialization section – Initializes loop variables before the loop begins
Variable update section – Resets loop variables each iteration
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

7. Undo | Redo
Workspace
Word in italics, Times Roman, identifies type of input desired. User input is non-italics, Courier.
FOR-EACH
gene IN
list
Control section – Determines form of iteration
Initialization section – Initializes loop variables before the loop begins
Variable update section – Resets loop variables each iteration
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

8. Undo | Redo
Workspace
Clicking hole (unfilled or not) selects it for both input (cursor appears) and replacement by a function.
FOR-EACH
gene IN |
Control section – Determines form of iteration
Initialization section – Initializes loop variables before the loop begins
Variable update section – Resets loop variables each iteration
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

9. Control section – Determines form of iteration
Analyysis
Components Gene-protein classes Sequence classes
Undo | Redo
Workspace
FOR-EACH
gene IN |
Control section – Determines form of iteration
Initialization section – Initializes loop variables before the loop begins
Variable update section – Resets loop variables each iteration
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

10. Control section – Determines form of iteration
Analyysis
Components Gene-protein classes Sequence classes
CODING-GENES-OF
COMMON-ORTHOLOGS-OF
GENES-OF
NONCODING-GENES-OF
PROTEINS-OF
Undo | Redo
Workspace
FOR-EACH
gene IN |
Control section – Determines form of iteration
Initialization section – Initializes loop variables before the loop begins
Variable update section – Resets loop variables each iteration
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

11. Control section – Determines form of iteration
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
organism-or-replicon-or-protein
Control section – Determines form of iteration
Initialization section – Initializes loop variables before the loop begins
Variable update section – Resets loop variables each iteration
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

12. No other iteration controls needed, so get rid of section.
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
A7120|
Control section – Determines form of iteration
Initialization section – Initializes loop variables before the loop begins
Variable update section – Resets loop variables each iteration
Body – Forms to be iterated
No other iteration controls needed, so get rid of section.
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

13. No initialization needed, so get rid of that section too.
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Initialization section – Initializes loop variables before the loop begins
Variable update section – Resets loop variables each iteration
Body – Forms to be iterated
Results section – Determines the result returned by the loop
No initialization needed, so get rid of that section too.
Final action – To be performed after last iteration
Results

14. Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Need to define the match for each gene, so open up variable update section.
Results

15. Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
Help Copy section Cut section
Delete section
ASSIGN variable
ASSIGN variable-list
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Section-specific possibilities appear below dashed line (ASSIGN maps to AS).
Results

16. Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
The variable match will be the specific sequence upstream from a gene that matches the pattern.
ASSIGN =
variable name
value
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

17. Variable update section – Resets loop variables each iteration
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN =
match|
value
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

18. Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
I just realized… I want to confine the search to upstream sequences of length > 20
ASSIGN =
match |
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

19. Variable update section – Resets loop variables each iteration
Logical comparison
Logical connectives
Loops and conditional executions Other logic functions
BOTH
EITHER
FOR-EACH IF
IF-NOT
LOOP
NOT
ORDER
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN =
match |
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

20. Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN =
match IF
condition
THEN
form
ELSE
form
Note that IF is built like FOR-EACH, consisting of a required argument plus two sections (dark cyano). The THEN section is required (so no X) but the ELSE block is optional.
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

21. Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN =
match IF |
THEN
form
ELSE
form
Another problem… I can't compare the length of the upstream region to 20 if the upstream region doesn't exist! (This happens when two genes are right next to each other). I need to protect against that possibility.
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

22. Variable update section – Resets loop variables each iteration
Logical comparison
Logical connectives
Loops and conditional executions Other logic functions
BOTH
EITHER
FOR-EACH IF
IF-NOT
LOOP
NOT
ORDER
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN =
match IF |
THEN
form
ELSE
form
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

23. Variable update section – Resets loop variables each iteration
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN =
match IF
BOTH AND
condition
THEN
form
ELSE
form
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

24. Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN =
match IF
BOTH AND
upseq|
condition
THEN
form
ELSE
form
Body – Forms to be iterated
I invent a variable upseq containing the upstream sequence, which must exist for the condition to be fulfilled. I'll worry later about defining it.
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

25. I want upseq's length (call it upseq-L) to be greater than 20.
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN =
match IF
BOTH AND
upseq |
THEN
form
ELSE
form
Body – Forms to be iterated
I want upseq's length (call it upseq-L) to be greater than 20.
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

26. Variable update section – Resets loop variables each iteration
Logical comparison
Logical connectives
Loops and conditional executions Other logic functions
BOTH
EITHER
FOR-EACH IF
IF-NOT
LOOP
NOT
ORDER
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN =
match IF
BOTH AND
upseq |
THEN
form
ELSE
form
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

27. Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
item
comparator
item =
THEN
form
ELSE
form
Here is a new category of things: Informational tokens (required choices). The token box has a title and a list of possible values. The box cannot be deleted.
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

28. Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
item
comparator
item
Help LESS-THAN SAME-AS GREATER-THAN =
THEN
form
ELSE
form
The is Windows convention to indicate more (but less likely) choices below.
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

29. Variable update section – Resets loop variables each iteration
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
item
GREATER-THAN
item =
THEN
form
ELSE
form
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

30. Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
eq-l|
GREATER-THAN
item =
THEN
form
ELSE
form
I type in the variable name, upseq-l, but since it's bigger than the box, the letters scroll.
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

31. Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN
20| =
THEN
form
If the condition is met, then I look for a match of the pattern in the upstream sequence.
ELSE
form
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

32. MATCH-OF is a function related to string analysis.
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN |
ELSE
form
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

33. Variable update section – Resets loop variables each iteration
Bioinformatic tools
String analysis
String extraction
String production
String type checks
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN |
ELSE
form
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

34. Variable update section – Resets loop variables each iteration
Bioinformatic tools
String analysis
String extraction
String production
String type checks
ALIGNMENT-OF
ALPHABET-OF BACKGROUND-FREQUENCIES-OF
COUNT-OF
GC-FRACTION-OF LENGTH-OF
MATCH-OF
MATCHES-OF
NUCLEOTIDE-DISTANCE
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN |
ELSE
form
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

35. Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
query type
query IN
target
ELSE
form
Here's another informational token box. Like option boxes, they're cyano, so users will not be tempted to fill them.
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

36. Variable update section – Resets loop variables each iteration
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
query type
query IN
target
Item
Pattern
Restriction enzyme
Slot value
ELSE
form
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

37. Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
query IN
target
ELSE
form
Input the pattern: "[AT]TGC.{8}CAT" i.e. A or T, then TGC, then eight unspecified, then CAT
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

38. Again, the string scrolls, because it's bigger than the box.
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
{8}CAT"| IN
target
ELSE
form
Again, the string scrolls, because it's bigger than the box.
The target is upseq, which I grab from a previous input box.
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

39. Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20
Help Copy
Cut Target for wrap =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
target
ELSE
form
Note the shortened menu. Only functions and global variables can be evaluated. Edit is not necessary any longer. Insert and Cut/insert strike me as too non-intuitive.
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

40. Variable update section – Resets loop variables each iteration
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
target
ELSE
form
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

41. Variable update section – Resets loop variables each iteration
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
target
Help Paste
Target for wrap
ELSE
form
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

42. No plans for the ELSE section, so delete it.
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
ELSE
form
No plans for the ELSE section, so delete it.
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

43. Ditto with Body section.
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Body – Forms to be iterated
Ditto with Body section.
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Results

44. When match exists, COLLECT it.
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop
When match exists, COLLECT it.
Final action – To be performed after last iteration
Results

45. Variable update section – Resets loop variables each iteration
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop
Help Delete section
APPEND COLLECT COUNT MAXIMIZE MINIMIZE SUM WHEN conditon …
UNLESS condition …
Final action – To be performed after last iteration
Results

46. Variable update section – Resets loop variables each iteration
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop
Help Delete section
APPEND COLLECT COUNT MAXIMIZE MINIMIZE SUM WHEN conditon …
UNLESS condition …
Final action – To be performed after last iteration
APPEND COLLECT COUNT MAXIMIZE MINIMIZE SUM
Results

47. Grab match from previous box.
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
Grab match from previous box.
condition
form
Final action – To be performed after last iteration
Results

48. Variable update section – Resets loop variables each iteration
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match
Help Copy
Cut Target for wrap IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
condition
form
Final action – To be performed after last iteration
Results

49. Variable update section – Resets loop variables each iteration
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
condition
form
Final action – To be performed after last iteration
Results

50. Variable update section – Resets loop variables each iteration
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
condition
Help Paste
Target for wrap
form
Final action – To be performed after last iteration
Results

51. Variable update section – Resets loop variables each iteration
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
match
form
Final action – To be performed after last iteration
Results

52. I want to save both the gene and the match, so I need a list.
Undo | Redo
I want to save both the gene and the match, so I need a list.
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
match |
Final action – To be performed after last iteration
Results

53. Variable update section – Resets loop variables each iteration
List / table analysis
List / table extraction
List / table production
List / table type-checks
LIST PART-OF
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
match |
Final action – To be performed after last iteration
Results

54. Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
match
LIST is described in the menu as the easily comprehended "LIST" but represented as the compact { } and is born empty.
{ }
Final action – To be performed after last iteration
Results

55. Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
Since LIST has no options, the arrow is used to generate new elements quickly
match
{ }
element
Final action – To be performed after last iteration
Results

56. Variable update section – Resets loop variables each iteration
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
match
{ }
element
element
Final action – To be performed after last iteration
Results

57. I recall that match is still copied, so I use it.
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
I recall that match is still copied, so I use it.
match
{ }
gene|
element
Final action – To be performed after last iteration
Results

58. I recall that match is still copied, so I use it.
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
I recall that match is still copied, so I use it.
match
{ }
gene|
element
Final action – To be performed after last iteration
Results

59. Variable update section – Resets loop variables each iteration
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
match
{ }
gene
element
Help Paste
Target for wrap
Final action – To be performed after last iteration
Results

60. Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
Housekeeping.
match
{ }
gene
match
Final action – To be performed after last iteration
Results

61. Finally the task of defining the two variables I invented on the fly.
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
Finally the task of defining the two variables I invented on the fly.
match
{ }
gene
match
Results

62. ASSIGN here places a new ASSIGN clause at the beginning of the list.
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
Help Clear section
Copy section
Cut section
Delete section
ASSIGN variable
ASSIGN variable-list
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
ASSIGN here places a new ASSIGN clause at the beginning of the list.
match
{ }
gene
match
Results

63. Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN =
variable name
value
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
Note that ASSIGN clauses are cyano, not yellow/orange, like functions, but they're a lighter shade, to set them apart from one another
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
match
{ }
gene
match
Results

64. Upseq will be given the SEQUENCE-UPSTREAM-OF the current gene.
Undo | Redo
Workspace
Upseq will be given the SEQUENCE-UPSTREAM-OF the current gene.
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN =
upseq|
value
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
match
{ }
gene
match
Results

65. Variable update section – Resets loop variables each iteration
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN =
upseq |
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
match
{ }
gene
match
Results

66. Variable update section – Resets loop variables each iteration
Descrtipion / analysis
Gene neighborhood
Gene / protein types
Translation
DESCRIPTION-OF
ORTHOLOG-OF SEQUENCE-OF
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN =
upseq |
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
match
{ }
gene
match
Results

67. Variable update section – Resets loop variables each iteration
Descrtipion / analysis
Gene neighborhood
Gene / protein types
Translation
DESCRIPTION-OF
ORTHOLOG-OF SEQUENCE-OF
CONTEXT-OF
GENE-DOWNSTREAM-OF
GENE-LEFT-OF
GENE-RIGHT-OF
GENE-UPSTREAM-OF
GENES-OF
SEQUENCE-DOWNSTREAM-OF
SEQUENCE-LEFT-OF
SEQUENCE-RIGHT-OF
SEQUENCE-UPSTREAM-OF
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN =
upseq |
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
match
{ }
gene
match
Results

68. Variable update section – Resets loop variables each iteration
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN =
upseq
SEQUENCE-UPSTREAM-OF
gene-or-protein
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
match
{ }
gene
match
Results

69. Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN =
upseq
SEQUENCE-UPSTREAM-OF
gene|
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
Now assign upseq-l.
match
{ }
gene
match
Results

70. Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN =
upseq
SEQUENCE-UPSTREAM-OF
gene
ASSIGN variable
ASSIGN variable-list
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
ASSIGN here places a new ASSIGN clause at the position of the arrow. It's therefore possible to put an ASSIGN anywhere
match
{ }
gene
match
Results

71. Variable update section – Resets loop variables each iteration
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN =
upseq
SEQUENCE-UPSTREAM-OF
gene
ASSIGN =
variable name
value
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
match
{ }
gene
match
Results

72. Variable update section – Resets loop variables each iteration
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN =
upseq
SEQUENCE-UPSTREAM-OF
gene
ASSIGN =
variable name
value
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20
Help Copy
Cut Target for wrap =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
match
{ }
gene
match
Results

73. Variable update section – Resets loop variables each iteration
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN =
upseq
SEQUENCE-UPSTREAM-OF
gene
ASSIGN =
variable name
value
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
match
{ }
gene
match
Results

74. Variable update section – Resets loop variables each iteration
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN =
upseq
SEQUENCE-UPSTREAM-OF
gene
ASSIGN =
variable name
value
Help Paste
Target for wrap
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
match
{ }
gene
match
Results

75. Variable update section – Resets loop variables each iteration
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN =
upseq
SEQUENCE-UPSTREAM-OF
gene
ASSIGN =
upseq-l
value
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
match
{ }
gene
match
Results

76. Upseq-l is given the length of the upstream sequence, upseq.
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN =
upseq
SEQUENCE-UPSTREAM-OF
gene
ASSIGN =
upseq-l |
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
match
{ }
gene
match
Results

77. Variable update section – Resets loop variables each iteration
Descrtipion / analysis
Gene neighborhood
Gene / protein types
Translation
DESCRIPTION-OF
ORTHOLOG-OF SEQUENCE-OF
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN =
upseq
SEQUENCE-UPSTREAM-OF
gene
ASSIGN =
upseq-l |
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
match
{ }
gene
match
Results

78. Variable update section – Resets loop variables each iteration
Descrtipion / analysis
Gene neighborhood
Gene / protein types
Translation
DESCRIPTION-OF
ORTHOLOG-OF SEQUENCE-OF
COG-ID-OF
DESCRIPTION-OF
ENCODES-PROTEIN?
GENE-DESCRIBED-BY
GENE-NAMED
GENE-OF
HYDROPHOBICITY-OF
LENGTH-OF
LENGTHS-OF
MW-OF
NAME-OF
ORTHOLOG-OF
PROTEIN-NAMED
PROTEIN-OF
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN =
upseq
SEQUENCE-UPSTREAM-OF
gene
ASSIGN =
upseq-l |
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
match
{ }
gene
match
Results

79. Variable update section – Resets loop variables each iteration
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN =
upseq
SEQUENCE-UPSTREAM-OF
gene
ASSIGN =
upseq-l
entity-or-list-or-string
LENGTH-OF
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
match
{ }
gene
match
Results

80. Variable update section – Resets loop variables each iteration
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN =
upseq
SEQUENCE-UPSTREAM-OF
gene
ASSIGN =
upseq-l
entity-or-list-or-string
LENGTH-OF
Help Paste
Target for wrap
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
match
{ }
gene
match
Results

81. Clicking the filled input box immediately opens it for editing
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN =
upseq
SEQUENCE-UPSTREAM-OF
gene
Clicking the filled input box immediately opens it for editing
ASSIGN =
upseq-l
LENGTH-OF
upseq-l
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
match
{ }
gene
match
Results

82. DONE! Execute.
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN =
upseq
SEQUENCE-UPSTREAM-OF
gene
ASSIGN =
upseq-l
LENGTH-OF
upseq-l |
ASSIGN
match IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
match
{ }
gene
match
Results

83. Variable update section – Resets loop variables each iteration
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
Help Execute
Copy
Cut Show code
Target for wrap
variable IN list
variable-list IN list of lists
variable FROM number
variable FROM number TO number
a7120
Variable update section – Resets loop variables each iteration
ASSIGN =
upseq
SEQUENCE-UPSTREAM-OF
gene
ASSIGN =
upseq-l
LENGTH-OF
upseq
ASSIGN
pattern IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
match
{ }
gene
match
Results

84. Compare
Click anywhere

85. Click anywhere Compare
Undo | Redo
Workspace
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN =
upseq
SEQUENCE-UPSTREAM-OF
gene
ASSIGN =
upseq-l
LENGTH-OF
upseq
ASSIGN
pattern IF
BOTH AND
upseq
ORDER
upseq-l
GREATER-THAN 20 =
THEN
MATCH-OF
PATTERN
"[AT]TGC{8}CAT" IN
upseq
Results section – Determines the result returned by the loop WHEN
COLLECT
match
{ }
gene
match
Results
Click anywhere

86. Proposed form of LOOP and IF - Some features:
FOR-EACH
gene IN
GENES-OF
a7120
Variable update section – Resets loop variables each iteration
ASSIGN =
match IF
condition
THEN
form
ELSE
form
Body – Forms to be iterated
Results section – Determines the result returned by the loop
Final action – To be performed after last iteration
Proposed form of LOOP and IF - Some features:
Sections are self-explained and set apart using same convention as keywords (cyano, no border) to indicate that it's nonfillable.
Informative token boxes
Wasteful of space, maximizes comprehensibility
END