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Changes between Version 8 and Version 9 of UTGBManual

Timestamp:: 08/15/07 15:55:11 (18 years ago)
Author:: leo
Comment:: --

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UTGBManual

-                      v8
+                      v9
  End:: Select the end point from your targeted sequence to display. The number should be 1-origin. If the ending point is greater than the starting point then the display will be normal. Otherwise, the display will be reverse. In both cases, the ending base will be included in the displaying sequence.
 ü         Width: Input the width in terms of pixels for output track display. Input the value that is suitable for your vision. Normally, it is assumed that width is equal to the screen width. It is also possible to input the width as 10 times bigger than the screen width. In that case, it seems to be convenient to use the scroll of the browser.
+ Width:: Input the width in terms of pixels for output track display. Input the value that is suitable for your vision. Normally, it is assumed that width is equal to the screen width. It is also possible to input the width as 10 times bigger than the screen width. In that case, it seems to be convenient to use the scroll of the browser.
 After manipulating the previous items, press the “Apply” button to shifting to the desired position of the sequence.
+Using shifting button method
+browser_moves.png
+=== Using shifting button method ===
+[[Image(browser_moves.png)]]
 Moreover, there is another method by using the button (like above image). Normally, the input box method is useful only when it is important to have the correct position of the sequence.  As number must be supplied in this method, sometime this process is quit cumbersome. So we provide more intuitive methods for your convenience. So the buttons related to these methods are as follows,
 ü         Shifting (rr.png,r.png,f.png,ff.png):  rr.png,r.png,f.png,ff.png are buttons to shifting the sequence. Therr.png button scrolls sequence up to one screen size where the r.png button scrolls half screen to the left. The inverse buttons are for shifting to the right.
 ü         Scaling (zoomout.png, zoomin.png, zoom10x.png, zoom1x.png, zoom01x.png, zoom001x.png, zoom0001x.png):  The zoomout.png button does scaling down and the display will be half of the present size where zoomin.png button does scaling up and the display will be 2 times bigger than present size. The fractional form button specifies the scale directly. The scaling unit is 1bp/pixel. For example, zoom1x.png means 1 bp is displayed by 1 pixel, whereas zoom01x.png means 10 bp is displayed by 1 pixel. So zoom10x.png means the scale that enlarges the display up to the base level. zoom0001x.png is a scale ratio useful in displaying 1M bps on the screen.  At the time of scaling up or down the view points of the present display will be remained unchanged.
+Using overview, ruler and zooming track method
+ Shifting ([[Image(rr.png)]],[[Image(r.png)]], [[Image(f.png)]],[[Image(ff.png)]]::  [[Image(rr.png), [[Image(r.png)]], [[Image(f.png)]],[[Image(ff.png)]] are buttons to shifting the sequence. Therr.png button scrolls sequence up to one screen size where the r.png button scrolls half screen to the left. The inverse buttons are for shifting to the right.
+ Scaling (zoomout.png, zoomin.png, zoom10x.png, zoom1x.png, zoom01x.png, zoom001x.png, zoom0001x.png):  The zoomout.png button does scaling down and the display will be half of the present size where zoomin.png button does scaling up and the display will be 2 times bigger than present size. The fractional form button specifies the scale directly. The scaling unit is 1bp/pixel. For example, zoom1x.png means 1 bp is displayed by 1 pixel, whereas zoom01x.png means 10 bp is displayed by 1 pixel. So zoom10x.png means the scale that enlarges the display up to the base level. zoom0001x.png is a scale ratio useful in displaying 1M bps on the screen.  At the time of scaling up or down the view points of the present display will be remained unchanged.
+=== Using overview, ruler and zooming track method ===
 In addition, there are some methods to shifting. These are overview, ruler, zooming trucks. You can shift the viewpoint by clicking any position of these tracks. For details, please refer to the respective details about the each track.
+.2. Functions of buttons
+ü         (rev)  You can display the sequence in reverse mode by UT Genome Browser. Normally a sequence is displayed from left to right but you can reverse it with the (rev) button. An alternative way to display in reverse way is to input “start” value greater than “end” value in the Input Box. The same task can be done easily by clicking the (rev) button. As the (rev) button reverses start and end points of the present displayed sequence so this can change the display mode from normal to reverse or vice versa. If you press the (fasta) button on reverse mode, then the complementary strand of displayed strand will be retrieved.
+ü         (top)  By pressing this button you can return to the main screen. Information about present displayed range, track and each track setting etc. will be preserved.
+ü         (clear)  By pressing this button you can return to the main screen. Information about present displayed range, track and each track setting etc. will be initialized.
+ü         (Track)  Addition, deletion, and rearranging can be performed by this button. Details description will be given later.
+ü         (fasta)  Present displaying sequence can be retrieved with this button in fasta format. You will be instructed to save as a file name. For example, Medaka-200406-scaffold429 (64587-66612). fasta
+.3. Addition, Deletion, and Rearrangement of Tracks
+browser_track.png
+== Functions of buttons ==
+ (rev)::  You can display the sequence in reverse mode by UT Genome Browser. Normally a sequence is displayed from left to right but you can reverse it with the (rev) button. An alternative way to display in reverse way is to input “start” value greater than “end” value in the Input Box. The same task can be done easily by clicking the (rev) button. As the (rev) button reverses start and end points of the present displayed sequence so this can change the display mode from normal to reverse or vice versa. If you press the (fasta) button on reverse mode, then the complementary strand of displayed strand will be retrieved.
+ (top)::  By pressing this button you can return to the main screen. Information about present displayed range, track and each track setting etc. will be preserved.
+ (clear)::  By pressing this button you can return to the main screen. Information about present displayed range, track and each track setting etc. will be initialized.
+ (Track)::  Addition, deletion, and rearranging can be performed by this button. Details description will be given later.
+ (fasta)::  Present displaying sequence can be retrieved with this button in fasta format. You will be instructed to save as a file name. For example, Medaka-200406-scaffold429 (64587-66612). fasta
+== Addition, Deletion, and Rearrangement of Tracks ==
+[[Image(browser_track.png)]]
 When the (track) button of the main screen is pressed, the above track-editing screen will pop up. Here you can do addition, deletion and rearrangement of the tracks. This editing screen can be divided into three parts - displaying tracks, removed tracks, and adding new track.
 ü         Displaying track: Here, tracks’ deletion and rearrangement can be done to the present displayed screen. The deleted tracks will be replaced to next removed track.
 ü         Removed track: This is the list of all tracks, which are deleted at Displaying Tracks. It is something like garbage bin. Undo-processing is possible for the tracks that are displayed here.
 ü         Add new track: New tracks, which are not available at present display, can be added by this track. By setting the URL of the new tracks, push add button. If the new tracks’ URL is read properly, the new tracks will be added after the present displayed tracks.
+.4. Setting for Tracks
+ Displaying track:: Here, tracks’ deletion and rearrangement can be done to the present displayed screen. The deleted tracks will be replaced to next removed track.
+ Removed track:: This is the list of all tracks, which are deleted at Displaying Tracks. It is something like garbage bin. Undo-processing is possible for the tracks that are displayed here.
+ Add new track:: New tracks, which are not available at present display, can be added by this track. By setting the URL of the new tracks, push add button. If the new tracks’ URL is read properly, the new tracks will be added after the present displayed tracks.
+=== Setting for Tracks ===
 On main screen, when the cfg.png button, beside the track name, is pressed, the display of that track can be customized as above image. The customizing contents of the tracks differ from each other. On the other hand, there are some tracks which contents cannot be customized at all. For details, please refer to the individual tracks information.
+. Pre-defined Tracks
+.1. Overview Track
+track_overview.png
+==  Pre-defined Tracks ==
+=== Overview Track ===
+[[Image(track_overview.png)]]
 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.
+.2. Ruler and Zooming Tracks
+=== Ruler and Zooming Tracks ===
 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.
 …
+.3. Base Color Track
+=== Base Color Track ===
 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).
 …
+.4. 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.
+.5. 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.
+.6. Mapped Gene Track
+=== Mapped Gene Track ===
 …
+Display setting
 If the 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
+=== 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 ===
 Predicted genes’ display setting can be changed here. There are four kinds of display style. These styles are full, pack, small and dense.
 ü         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.
 ü         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.
 ü         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.
 ü         Dense: In this style, only the positions of aligned exons are displayed on one line.
+ 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.
+ 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.
+ 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.
+ Dense:: In this style, only the positions of aligned exons are displayed on one line.
 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
 Here, you can fix which development stage’s expression EST should be displayed.
 Stage color 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
+ * 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.
+.7. 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.
 Display settings
+ * Display settings
 If the cfg.png mark button on the left side of Genscan Track is clicked, the display setting will pop up. Here are the details of this setting.
 Style selects setting
+ * Style selects setting
 Predicted genes’ display setting can be changed here. There are four kinds of display style. These styles are full, pack, small and dense, and they are similar to those styles in Mapped Gene Track.
 Linkage of each gene
+ * Linkage of each gene
 In full, pack and small style each gene can be clicked on. After clicking each gene, the details of prediction by Genscan will be appeared.
+.8. Comparative Genomics Track
 Fugu Scaffold track
 Description
+=== Comparative Genomics Track ===
+ * Fugu Scaffold track
+ * Description
 This track shows Fugu/Medaka homologous scaffolds detected by ALPS alignment program. Fugu scaffolds are denoted by boxes connected by arrows. The boxes represent regions of high homology (match ratio > 60%) aligned by ALPS. The arrows represent low homology regions or gaps in Fugu scaffold.  The direction of arrows indicates the orientation of Fugu/Medaka alignments. Clicking on a Fugu scaffold will open a new window to display its dotplot with Fugu scaffold sequence provided in the same page.  The Fugu sequence (Fugu v.2.0) was downloaded from JGI.
 Method
+ * Method
 Fugu scaffold sequences are split into non-overlapping 300mer sequences and these 300mer sequences are mapped to Medaka scaffolds with ALPS. ALPS alignments with match ratio less than 60% are discarded and remaining alignments are chained by longest monotone subsequence algorithm. Chains consist of more than 10 alignments are displayed in the track. Note that inversions or microrearrangements are not shown. Only the longest monotone subsequence is displayed for each Fugu scaffold.
 Linkage of each scaffold
+ * Linkage of each scaffold
 In full, pack and small style each gene can be clicked on. After clicking each scaffold, the detailed alignments will be appeared as like dot plot. Dotplot shows homologous regions of Fugu/Medaka scaffolds as diagonal runs of dots. Each dot, plotted based on sequence similarity score, indicates that significantly many seed matches are found between corresponding regions. The sequence similarity score is defined in such a way that tandem repeats are not assigned high scores while unique sequences are assigned high scores.
 …
+Ramen Assembler / UT Genome Browser Team Members
+= Ramen Assembler / UT Genome Browser Team Members =
 Ramen Genome Assembler Development Team
 ü         Development of “Ramen” genome assembler and assembly of medaka genome:
+ * Development of “Ramen” genome assembler and assembly of medaka genome:
 Masahiro Kasahara and Shin Sasaki
 ü         Development of “Ramen Viewer” for genome assembly:
+ * Development of “Ramen Viewer” for genome assembly:
 Yukinobu Nagayasu
 …
 UT Genome Browser Development Team
 ü         Design and development of UT Genome Browser, keyword search function, libraries for describing tracks:
+ * Design and development of UT Genome Browser, keyword search function, libraries for describing tracks:
 Yukinobu Nagayasu and Koichiro Doi
 ü         Online mapping function for query sequences:
+ * Online mapping function for query sequences:
 Tomoyuki Yamada
 ü         Comparative Genomics Track:
+ * Comparative Genomics Track:
 Yoichiro Nakatani and Wei Qu
 ü         Gene Prediction:
+ * Gene Prediction:
 Ahsan Budrul
 ü         Mapped Gene Track:
+ * Mapped Gene Track:
 Yasuhiro Kasai
 ü         Database access accelerators:
+ * Database access accelerators:
 Takehiro Furudate and Atsushi Mori
 ü         Overall management:
+ * Overall management:
 Koichiro Doi and Shinichi Morishita
+Acknowledgements
+= Acknowledgements =