Changes between Version 50 and Version 51 of UTGBManual

Timestamp:

09/06/07 16:53:35 (18 years ago)

Author:

kobayashi

Comment:

--

UTGBManual

@@ -72 +72 @@
 You can input values into the input boxes (like above image) inside the main window. The details about this method are as follows,
 
- Species:: Select the species to display. The selectable revisions would be changed with respect to the species. At present, only Medaka is possible to be selected.
-
- Revision:: Select the revision of the target specie’s genome. The selecting topics will change with respect to the selected revision.
-
- Target:: Select the target region to be displayed, from the selected species and selected revision. In the case of 200406 revision of Medaka, only scaffold name (e.g. scaffold123) can be selected but not the chromosome name (e.g. chr10). Chromosome numbers will be available in our later revision.
-
- Start:: Select the start position from your targeted sequence to display. The number should be 1-origin (i.e. the starting point will be 1).
-
- End:: Select the end point from your targeted sequence to display. The number should be 1-origin. If the ending point is greater than the starting point then the display will be normal. Otherwise, the display will be reverse. In both cases, the ending base will be included in the displaying sequence.
+ Species:: At present, only Medaka is possible to be selected.
+
+ Revision:: Select the revision of genome assembly.
+
+ Start:: Select the start position of the scaffold to display.
+
+ End:: Select the end point of the scsaffold to display.If the ending point is greater than the starting point then the display will be normal.
 
  Width:: Input the width in terms of pixels for output track display. Input the value that is suitable for your vision. Normally, it is assumed that width is equal to the screen width. It is also possible to input the width as 10 times bigger than the screen width. In that case, it seems to be convenient to use the scroll of the browser.
@@ -111 +109 @@
  (rev)::  You can display the sequence in reverse mode by UT Genome Browser. Normally a sequence is displayed from left to right but you can reverse it with the (rev) button. An alternative way to display in reverse way is to input “start” value greater than “end” value in the Input Box. The same task can be done easily by clicking the (rev) button. As the (rev) button reverses start and end points of the present displayed sequence so this can change the display mode from normal to reverse or vice versa. If you press the (fasta) button on reverse mode, then the complementary strand of displayed strand will be retrieved.
 
- (top)::  By pressing this button you can return to the main screen. Information about present displayed range, track and each track setting etc. will be preserved.
-
- (track)::  Addition, deletion, and rearranging can be performed by this button. Details description will be given later.
-
- (fasta)::  Present displaying sequence can be retrieved with this button in fasta format. You will be instructed to save as a file name. For example, Medaka-200406-scaffold429 (64587-66612). fasta
+ (top)::  By pressing this button, you can return to the top page. 
+
+ (track)::  Track prerarion window will appear. Details description will be given below.
+
+ (fasta)::  Present displaying sequence can be retrieved with this button in fasta format. You will be instructed to save as a file name, Medaka-revision-scaffold# (start-end).fasta. e.g. Medaka-version1.0-scaffold12 (345-6789). fasta
 
  (png)::  Screen shot can be retrieved with this button in PNG format. Click to open the screen shot, and then save the image by right click and save. In some browser, the image will be saved as a BMP format.
@@ -166 +164 @@
  [[Image(pack.jpg)]]
 
- '''Small''':: In small style, object alignment is tha same as the pack style with smaller iages. Object names are not shown in this style.
+ '''Small''':: In small style, object allocation is tha same as the pack style with smaller iages. Object names are not shown in this style.
 
  [[Image(small.jpg)]]