Changes between Version 20 and Version 21 of UTGBManual

Timestamp:

08/15/07 16:53:32 (18 years ago)

Author:

leo

Comment:

--

UTGBManual

@@ -148 +148 @@
 == Ruler and Zooming Tracks ==
 
+[[Image(image029.jpg)]]
+[[Image(image030.jpg)]]
+
 Both the ruler track and the zooming track are displaying same contents with different color. These two show the base position number of the present displayed content with respect to the total sequence.  If you click any position of the ruler track, the viewpoint will move to the middle position. For example, if the rightmost end of the ruler track is clicked then the same effect will be happed as the ff.png button of main screen is pressed. Before using the zoom button on main screen, it is better to have the required region on middle position by using the ruler track to smoothing future enlarge processing.
 
@@ -155 +158 @@
 == Base Color Track ==
 
+[[Image(image032.jpg)]]
+[[Image(image033.jpg)]]
+
 Base color track changes the sequence to color mode. All four ATGC bases are displayed by converting to the individual color. It is natural to display each base pair by one pixel. By zooming in, you can see any specific region of the sequence in alphabet symbol (above bottom image).
 
@@ -162 +168 @@
 == Gap Track ==
 
+[[Image(image034.jpg)]]
+
 Gap Track is a track that displays gaps in a scaffold. By clicking any place except the gap, we can get the whole contig sequence in FASTA format. It is different from the (fasta) button in the main window, because it does not retrieve the displayed sequence only, but saves the whole contig sequence.
 
@@ -167 +175 @@
 == GC Content Track ==
 
+[[Image(image035.jpg)]]
+
 This track displays the ratio of GC contents for 5 pixels. If the pixel number of a base pair is more than 5, the coloring will be done to tell whether it is GC or AT.
 
@@ -172 +182 @@
 == Mapped Gene Track == 
 
+[[Image(image036.jpg)]]
+
 This track displays the mapping result of Fugu, Zebra fish and Medaka’s Est to the Medaka genome, done by ALPS (http://alps.gi.k.u-tokyo.ac.jp). The mapping region for the gene is displayed by line and the exons are shown in rectangular box. The arrow sign shows the plus or minus strand of the genome. The above image displays Medaka’s ESTs in black color, while the green color indicates cDNAs of Fugu. The current data sources of mapped genes are Medaka Unigene Build#10, Zebra fish Unigene Build#71, and Fugu ensemble pufferfish v21.2.c1( 10th May, 2004). We will revise the alignment periodically in response to the update of the data sources.
 
  
 = Display setting =
+[[Image(image037.jpg)]]
 
 If the [[Image(cfg.png)]] button on the left side of Mapped Gene Track is pressed, the display setting windows will pop up. There are three parts of this setting; namely, changing the total display style, alternating the mapping results if a gene will be displayed or not, and modifying the color of a gene. The setting, whether to show or not, will display all which fulfill the conditions. The color setting can be done by “use this color” button beside the track. 
@@ -184 +197 @@
 
  Full:: In full style, each gene’s position is displayed on one line. On left side the Genebank accession number or Ensemble Gene ID is written.
+ [[Image(image038.jpg)]]
 
  Pack:: By showing individual alignments together with the names (Genebank Acc or Ensemble Gene ID) of genes on left side in multiple on one line, the pack style is more compact than full style.
+ [[Image(image039.jpg)]]
 
  Small:: In small style, the up and down spaces for one gene are reduced to the minimum. Unlike the full style and the pack style, this does not display the names of the genes.
+ [[Image(image040.jpg)]]
 
  Dense:: In this style, only the positions of aligned exons are displayed on one line.
+ [[Image(image041.jpg)]]
 
 At present except the full style, if the numbers of the mapped genes are more than 200 in a range of more than 50kbp, the graphical view of the genes will be displayed.