Changes between Version 11 and Version 12 of UTGBManual

Timestamp:

08/15/07 16:12:38 (18 years ago)

Author:

leo

Comment:

--

UTGBManual

@@ -156 +156 @@
 
  
-=== Gap Track ===
+== Gap Track ==
 
 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.
 
  
-=== GC Content Track ===
+== GC Content Track ==
 
 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.
 
  
-=== Mapped Gene Track ===
- 
+== Mapped Gene Track == 
 
 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 ===
+= Display setting =
 
 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. 
 
-=== Style select setting ===
+== Style select setting ==
 
 Predicted genes’ display setting can be changed here. There are four kinds of display style. These styles are full, pack, small and dense.
@@ -190 +189 @@
 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.
 
- * FormSpecies disp setting
+=== FormSpecies disp setting ===
 
 Here we can set which species among Medaka, Zebra fish, Fugu’s mapping results are displayed or not. On default, all species results will be displayed. Only the species, which are checked on the Checkbook, will be displayed.      
 
- * FromSpecies color setting
+=== FromSpecies color setting ===
 
 The color distinguishing for Medaka, Zebra fish, Fugu’s can be done here.
 
- * MatchRatio gradation setting
+=== MatchRatio gradation setting ===
 
 Gene’s color can be changed with respect to its match ratio. Provided colors for the match ratios 0.7 and 1.0 respectively, the system automatically gradates the coloring of the alignments between the lower and upper match ratios.  
 
- * MatchRatio ulbound setting
+=== MatchRatio ulbound setting ===
 
 You can specify the range of the mapping ratio by inputting the lower and upper bounds into the corresponding boxes. Alignments of match ratios within the range are only displayed.
 
- * CoverRatio gradation setting
+=== CoverRatio gradation setting ===
 
 Gene’s color can also be changed with respect to its cover ratio. Provided colors for the cover ratios 0.4 and 1.0 respectively, the system automatically gradates the coloring of the alignments between the lower and upper cover ratios.  
 
- * CoverRatio ulbound setting
+=== CoverRatio ulbound setting ===
 
 You can specify the range of the cover ratio by inputting the lower and upper bounds into the corresponding boxes. Alignments of cover ratios within the range are only displayed.
 
- * Stage disp setting
+=== Stage disp setting ===
 
  * Here, you can fix which development stage’s expression EST should be displayed. 
 
- * Stage color setting
-
-Color distinguishing can be done with respect to development stage.
-
- 
- * Linkage for each gene 
+=== Stage color setting ===
+ 
+ * Color distinguishing can be done with respect to development stage.
+
+=== Linkage for each gene ===
 
 In full, pack and small style, each gene can be clicked on. By clicking each gene, you can see the details of this gene.
 
  
-===  Genscan Track ===
+== Genscan Track ==
 
 This track displays the predicted genes by Genscan. The predicted genes are viewed on lines, where the exons parts are on rectangular shape. Arrow sign presents the strand of the genes. The above image shows the predicted genes in pack style.
@@ -245 +243 @@
 
  
-=== Comparative Genomics Track ===
+== Comparative Genomics Track ==
 
  * Fugu Scaffold track