Changes between Version 47 and Version 48 of UTGBMedaka/Track
- Timestamp:
- 09/05/07 15:51:23 (18 years ago)
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UTGBMedaka/Track
v47 v48 4 4 5 5 [[PageOutline]] 6 == Chromosome Overview == 7 [[Image(ChromosomeOverView.jpg)]] 6 8 7 == Overview Track == 9 This track shows the location of presently displayed scaffold on the chromosome. In the above image, for instance, the blue-colored box shows the position of scaffold100 on chromosome 6, which is represented in the yellow bar. Click on any position of this track will bring you to the chromosome view (see below). The next scaffolds are indicated at the both end of yellow bar. Click on the scaffold name shown in light blue to move to the view of the corresponding scaffold. 8 10 9 [[Image(track_overview.png)]] 11 The details of this track is described here: http://medaka3.utgenome.org/~kobayashi/UTGBmedakaHELP/ChromosomeOverView.html 10 12 11 This track shows the range of present displayed window in the total genome. In above image, for instance, the blue-colored viewpoint shows the range from 125kb to 145kb. Clicking on any position of this overview track moves the viewpoint the middle position. For example, when you click on around 100k positions, the viewpoint will move to 90k-110k.12 13 14 13 == Ruler and Zooming Tracks == 15 14 … … 33 32 It is also possible to customize the corresponding base pair color also. For example, if GC base pair are only colored then we can use it as a simple GC content track. To get the sequence itself, it is better to save from fasta track. 34 33 35 36 == GC Content Track == 37 38 [[Image(image035.jpg)]] 39 40 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. 41 42 43 == Predicted Gene Track == 44 45 [[Image(pred.png)]] 46 47 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. 48 49 == 5’SAGE Track == 50 51 [[Image(5sage.png)]] 52 53 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. 54 55 == Sequence Quality Track == 34 == Quality Value Track == 56 35 57 36 [[Image(qv.png)]] … … 65 44 This track displays coverage ratio of a specific sequence from a scaffold, determined by aligning Plasmid read sequence on genome. 66 45 67 == Fosmid End Track ==46 == GC Content Track == 68 47 69 About 37.5 kb length Fosmids were obtained at the National Institute of Genetics (NIG,Japan). Finally, 217,344 fosmid end pairs (11.1 x clone coverage) successfully located on the genome. Mapped fosmid is viewed in UTGB(medaka) main window named as “Fosmid end Track” 70 [[Image(fosmid.png)]] 48 [[Image(image035.jpg)]] 71 49 72 This track displays all the mapped fosmid reads obtained at the National Institute of Genetics(NIG,Japan) by using rectangular box in a line. 50 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. 51 52 == Repeat Masker Track == 53 54 [[Image(repeat.png)]] 55 56 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. 73 57 74 58 == Bac End Track == … … 80 64 NCBI-BLAST (The parameters were all default, except the e-value threshold was set to 1e-10) 81 65 66 [[Image(bac.png)]] 82 67 83 [[Image(bac.png)]] 68 == Fosmid End Track == 69 70 About 37.5 kb length Fosmids were obtained at the National Institute of Genetics (NIG,Japan). Finally, 217,344 fosmid end pairs (11.1 x clone coverage) successfully located on the genome. Mapped fosmid is viewed in UTGB(medaka) main window named as “Fosmid end Track” 71 [[Image(fosmid.png)]] 72 73 This track displays all the mapped fosmid reads obtained at the National Institute of Genetics(NIG,Japan) by using rectangular box in a line. 84 74 85 75 == Genetic Marker Tracks == 86 76 87 77 Three tracks provide genetic marker information of medaka genome. 78 79 '''mappedGeneticMarkers''' 80 81 This track shows genetic markers whuch are used in medaka genome project (2, 3). 82 Click on an individual marker within a track opens a typing panel using Hd-rR/HNI female backcross panel. 83 84 [[Image(geneticmarker.jpg)]] 88 85 89 86 '''Mbase marker''' … … 93 90 94 91 [[Image(Mbase.jpg)]] 95 96 '''mappedGeneticMarkers'''97 98 This track shows genetic markers whuch are used in medaka genome project (2, 3).99 Click on an individual marker within a track opens a typing panel using Hd-rR/HNI female backcross panel.100 101 [[Image(geneticmarker.jpg)]]102 92 103 93 '''SSLP Marker''' … … 116 106 (3) Kimura ''et al.'', Gene 363 24-31 (2005)[[BR]] 117 107 (4) Kasahara ''et al.'', Nature 447:714-719 (2007) 118 119 == Repeat Element Track ==120 121 [[Image(repeat.png)]]122 123 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.124 108 125 109 == HNI alignment Track == … … 148 132 The details of this track is described here: http://medaka3.utgenome.org/~ssksn/HNI_SNPs/common/HNI_SNPs_description.html 149 133 150 == Ensembel Predicted geneTrack ==134 == 5’SAGE Track == 151 135 152 [[Image( Entra.jpg)]]136 [[Image(5sage.png)]] 153 137 154 This track displays medaka genes predicted on Ensembel(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.138 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. 155 139 156 This track is an alias of the Ensembl transcript model predictions in http://www.ensembl.org/Oryzias_latipes/index.html Ensembl Medaka. The mapping region for the gene is displayed by line and the exons are shown in rectangular box. The arrow shows the direction of the predicted transcript. 140 == Predicted Gene Track == 157 141 158 The current data sources are Ensembl44. 142 [[Image(pred.png)]] 159 143 160 Click each transcript for more imformation in Ensembl. 161 162 == Homology Track == 163 [[Image(homo.jpg)]] 164 165 Homologues genes of medaka-human, medaka-zebrafish, medaka-tetraodon, medaka-fugu are displayed in different tracks. 166 167 * EnsemblZFHomo: Zebrafish homologue 168 * !EnsemblMouseHomo: Mouse homologue 169 * !EnsemblHumanHomo: Human homologue 170 * !EnsemblFuguHomo: Fugu homologue 171 * !EnsemblTetraodonHomo: Tetraodon homologue 172 173 174 These track show olthologous genes, which are a result of the Ensembl homologue prediction. 175 The current data source is Ensembl44. 176 177 == Chromosome Overview == 178 [[Image(ChromosomeOverView.jpg)]] 179 180 This track shows the location of presently displayed scaffold on the chromosome. In the above image, for instance, the blue-colored box shows the position of scaffold100 on chromosome 6, which is represented in the yellow bar. Click on any position of this track will bring you to the chromosome view (see below). The next scaffolds are indicated at the both end of yellow bar. Click on the scaffold name shown in light blue to move to the view of the corresponding scaffold. 181 182 The details of this track is described here: http://medaka3.utgenome.org/~kobayashi/UTGBmedakaHELP/ChromosomeOverView.html 183 144 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. 184 145 185 146 == Medaka Trasncripts == … … 196 157 1. Florea,L., Hartzell,G., Zhang,Z., Rubin,G.M. and Miller,W. (1998) Computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res., 8: 967.974. 197 158 159 == Ensembel Predicted gene Track == 160 161 [[Image(Entra.jpg)]] 162 163 This track displays medaka genes predicted on Ensembel(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. 164 165 This track is an alias of the Ensembl transcript model predictions in http://www.ensembl.org/Oryzias_latipes/index.html Ensembl Medaka. The mapping region for the gene is displayed by line and the exons are shown in rectangular box. The arrow shows the direction of the predicted transcript. 166 167 The current data sources are Ensembl44. 168 169 Click each transcript for more imformation in Ensembl. 170 198 171 == Mutant_Track (under construction)== 199 172
