Changes between Version 4 and Version 5 of UTGBManual
- Timestamp:
- 08/15/07 15:29:53 (18 years ago)
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UTGBManual
v4 v5 1 1 = UTGB Manual = 2 2 3 1. Welcome 3 == Welcome == 4 4 5 5 Welcome to UT Genome Browser (University of Tokyo Genome Browser). With this browser you can browse genomic information of a target species (at present Medaka only) from several aspects. For example, the following tasks can be performed with different combinations. 6 6 7 ü You can search gene, by gene name, clone name, cluster name and display its surroundings gene groups. 8 9 ü You can map a genomic sequence to any genome and observe its surroundings. 10 11 ü You can save the sequence itself on your system from here. 7 * You can search gene, by gene name, clone name, cluster name and display its surroundings gene groups. 8 * You can map a genomic sequence to any genome and observe its surroundings. 9 * You can save the sequence itself on your system from here. 12 10 13 11 Questions, suggestions or comments are welcome to webmaster@utgenome.org. 14 12 15 16 2. Keyword Search 17 18 keyword_top.png 19 20 13 == Keyword Search == 14 15 [[Image(keyword_top.png)]] 21 16 22 17 The top window displays the keyword search engine, as above picture illustrates. Inputting any keyword at the query box, we can see the detail information about the query. More about keyword search can be found in the help, written on the same window. In addition, if the keyword is a part of targets, then all the targets will be displayed. For example, the keyword “BCD” will match to “ABCD”, “BCDE”, “BCD” and “BCDF” etc. (this is worked out with using a suffix array.) 23 18 24 25 2.1. Gene List 26 27 keyword_genes.png 28 29 19 === Gene List === 20 21 [[Image(keyword_genes.png)]] 30 22 31 23 When there are many genes for one keyword search, all genes will be displayed on a list. Pressing the (*) button on the left side, you can go to the mapped region for the gene. This list appears when multiple candidate entries are found, typically when class names or part of a gene number are input as a keyword. If a Genebank accession number is given, the number must be unique, and hence this list does not appear. 32 24 33 25 34 2.2. Mapping Position List 35 36 keyword_locs.png 37 38 26 === Mapping Position List === 27 28 [[Image(keyword_locs.png)]] 39 29 40 30 If the query gene has mapped to several regions on the genomic sequence, the list of all positions will be shown. Pressing the (*) button on the left side displays the mapped region of the gene. If there is only one mapped region of the gene, the list is skipped to display. 41 31 42 32 43 3. Sequence Alignment 44 45 online01.PNG 46 47 33 == Sequence Alignment == 34 35 [[Image(online01.PNG)]] 48 36 49 37 Sequence mapping is possible by inputting a sequence in the online mapping frame (above image) at the bottom of the main window. After selecting the species and its revision, press the search button on the bottom. The request is sent to the alignment server ALPS to align the given sequence to the selected genome. Afterwards, the list of alignment results is returned if the system finds some alignments. 50 38 51 52 53 online02.PNG 39 [[Image(online02.PNG)]] 54 40 55 41 From the list, you can select one alignment by clicking the result button as illustrated above. Then, the aligned result will appear on the browser. The ALPS mapping track in following snapshot displays the added mapping status. 56 42 57 58 59 online03.PNG 60 4. Main Window 61 62 browser_main.png 63 64 43 44 [[Image(online03.PNG)]] 45 46 == Main Window == 47 48 [[Image(browser_main.png)]] 65 49 66 50 The above picture shows the main screen for UT Genome Browser. It is possible to see the targeted region of genomic sequence by many tracks. This browser provides the following functions to manipulate tracks on this image screen. 67 51 68 ü Shifting, zooming in and out, and reversing of the target region. It facilitates zooming in the sequence until bases can be seen, while providing a panoramic, structural view for the sequence. 69 70 ü Adding, deleting and reordering the tracks. 71 72 ü Customizing of each track’s display. 73 74 ü Retrieving the present displayed sequence in Fasta format. 75 76 ü Continuing keyword search. 52 * Shifting, zooming in and out, and reversing of the target region. It facilitates zooming in the sequence until bases can be seen, while providing a panoramic, structural view for the sequence. 53 * Adding, deleting and reordering the tracks. 54 * Customizing of each track’s display. 55 * Retrieving the present displayed sequence in Fasta format. 56 * Continuing keyword search. 77 57 78 58 In what follows, we describe the detail about each function. 79 80 81 4.1 Scrolling and zooming the main window 59 60 === Scrolling and zooming the main window === 82 61 83 62 On main window, it is possible to shift and to zoom in/out the present observing sequence. These tasks can be carried out by:
