Changes between Version 77 and Version 78 of UTGBMedaka/Track

Timestamp:

09/10/07 16:08:28 (18 years ago)

Author:

yamada

Comment:

--

UTGBMedaka/Track

@@ -96 +96 @@
 '''mappedGeneticMarkers''' 
 
-This track shows genetic markers whuch are used in medaka genome project (2, 3).
+This track shows genetic markers which are used in medaka genome project (2, 3).
 Click on an individual marker within a track opens a table of typing data using Hd-rR/HNI female backcross panel.
 
@@ -186 +186 @@
 [[Image(MedakaTranscriptsSc150.jpg)]]
 
-This track shows a total set of medaka transcripts from [http://www.ncbi.nlm.nih.gov/UniGene/UGOrg.cgi?TAXID=8090 Unigne database build#19] in ncbi. Transcripts are initially aligned using BLASTN and listed the scaffolds which show the best match. The final alignments were produced between transcrips and the selected scaffolds using sim4, a program to align cDNA and genomic DNA (ref. 1). In some case, transcripts are mapped to unexpectedlly huge region because of the low complexity sequences in the transcripts. We eliminated these regions when the mapped region is over 200 kb.  
+This track shows a total set of medaka transcripts from [http://www.ncbi.nlm.nih.gov/UniGene/UGOrg.cgi?TAXID=8090 Unigne database build#19] in ncbi. Transcripts are initially aligned using BLASTN and listed the scaffolds which show the best match. The final alignments were produced between transcripts and the selected scaffolds using sim4, a program to align cDNA and genomic DNA (ref. 1). In some case, transcripts are mapped to unexpectedly huge region because of the low complexity sequences in the transcripts. We eliminated these regions when the mapped region is over 200 kb.  
 
 Black-colored boxes indicate aligned regions and bars indicate gaps. Arrows indicate the transcription directions.  Click on each transcript opens a link to the information in the NCBI nucleotide database.
@@ -220 +220 @@
 [[Image(ChrView.jpg)]] 
 
-This track is not a regular track in the main window. This track opens when you search choromosome from keyword seach (select medaka-chr). You can also access this track from Chromosome OverView track (see above) as a link. This track shows the relationship among chromosome, scaffolds and genetic markers.
-
-The initial view is very busy, however, you can zoom into any region. It is also helpful to set width large, such as 10000.  As shown in the figure below, you can obtain the information how the neibouring scaffolds are ordered by genetic markers. Genetic distance among the genetic markers are shown. The color of the lines which represent genetic markers is changed where recombination is observed between the neibouring markers.
-
-There are three types of scaffolds, unorderd, unoriented and mapped. Unorderd means the cluster of the scaffold. These scaffolds are not segregated by genetic markers and mapped on the same region. Unoriented means the sololy mapped scaffold without the directional information. Mapped means the scaffold that is sololy and directionally mapped scaffolds. If two scaffolds are linked by sigle BAC clone and it is consistent with genetic marker inforamation, two scaffold are shown to be connected with holizontal line (ultracontig).  Kunming means a typing panel only used to map scaffolds on chromosome 11.
+This track is not a regular track in the main window. This track opens when you search chromosome from keyword seach (select medaka-chr). You can also access this track from Chromosome OverView track (see above) as a link. This track shows the relationship among chromosome, scaffolds and genetic markers.
+
+The initial view is very busy, however, you can zoom into any region. It is also helpful to set width large, such as 10000.  As shown in the figure below, you can obtain the information how the neighbouring scaffolds are ordered by genetic markers. Genetic distances among the genetic markers are shown. The color of the lines which represent genetic markers is changed where recombination is observed between the neighbouring markers.
+
+There are three types of scaffolds, unorderd, unoriented and mapped. Unorderd means the cluster of the scaffolds. These scaffolds are not segregated by genetic markers and mapped on the same region. Unoriented means the sololy mapped scaffold without the directional information. Mapped means the scaffold that is sololy and directionally mapped scaffolds. If two scaffolds are linked by sigle BAC clone and it is consistent with genetic marker inforamation, two scaffolds are shown to be connected with horizontal line (ultracontig).  Kunming means a typing panel only used to map scaffolds on chromosome 11.
 
 [[Image(chr_scroll.jpg)]]