Changes between Version 23 and Version 24 of UTGBManual

Timestamp:

08/15/07 17:02:34 (18 years ago)

Author:

leo

Comment:

--

UTGBManual

@@ -181 +181 @@
 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.
 
- 
+== Predicted Gene Track ==
+
+This track displays the medaka predicted genes as Mapped gene track. It is viewed on lines, where the exons parts are on rectangular shape. Arrow sign shows the plus or minus strand of the genome.
+
+== 5’SAGE track ==
+ This track displays the medaka expression profile by showing mapped 5’end tag of an expressed Gene. Details of each tag can be found by clicking on each viewed rectangle on this track. 
+
+== Sequence quality track ==
+This track presents the quality value of medaka assembled sequences. The quality value of a subsequence in a scaffold can be viewed by inserting sequence’s scaffold name and location on main window.
+
+== Coverage track ==
+This track displays coverage ratio of a specific sequence from a scaffold, determined by aligning Plasmid read sequence on genome.
+ 
+== Fosmid End Track == 
+        This track displays all the mapped fosmid reads obtained at the National Institute of Genetics(NIG,Japan) by using rectangular box in a line. 
+
+== Bac End Track ==
+        
+== RFLP marker Track ==
+        This track presents known Restriction Fragment Length Polymorphism (RFLP) marker downloaded from () and mapped to medaka genomic sequence. 
+
+== Repeat Element Track ==
+        This track displays all the repeat elements in medaka genome fixed by repeatmasker (ref), RepBase(ref) and de novo repeat finding tool(ref). The repeat element’s region is displayed by a rectangular box. 
+ 
+== HNI alignment Track ==
+        This track displays all the polymorphisms regions between medaka Hd-rR and HNI strain. 
+
+== Ensembel Predicted gene Track ==
+        This track displays medaka genes predicted on Enembel(ref) pipe line. The gene region is displayed by line and the bac ends are shown in rectangular box. The arrow sign shows the plus or minus strand of the genome. 
+
+== Homology Track ==
+        Homologues genes of medaka-human, medaka-zebrafish, medaka-tetraodon, medaka-fugu are displayed in different tracks.
+
 = Display setting =
 [[Image(image037.jpg)]]