Posted: 2017-12-07 14:25
RankVista regions are colored according to their annotation, as seen in Fig. 5. Note that RankVista coloring is based on exon annotations of all aligned sequences, not just the one currently used as the base. Consequently, an unannotated region in the base sequence might still be colored as an exon because of annotations from other sequences. In another deviation from the standard scheme, RankVISTA colors UTRs and coding exons the same, since they are treated identically by Gumby.
The browser shows base genome annotation directly above the curves (Fig. 8). Arrows signifying genes are drawn above the graphs, pointing in the direction of the gene. All exons and UTRs are marked with the same colors as on the VISTA graph. Gene names appear underneath the arrows if there is enough room. Repeats are shown below the genes, colored according to the legend in the lower left-hand corner of the display. SNPs , if they exist, are shown directly above the graphs. This track contains dbSNP, available from /snp. When viewing the track at or near base-level resolution, the displayed width of the SNP corresponds to the width of the variant in the reference sequence. On a large region the darkness of a SNP mark corresponds to the SNPs density on this region. SNPs are also indicated on base-pair level alignment panel.
In addition to navigating the browser by entering exact coordinates in the position control panel and searching by gene names, the browser provides all the standard scrolling and functions. To move left or right by half the size of the current region, click the scroll left/right buttons. To in, click the in button or highlight the area you want to see in detail by holding down the left mouse button while moving the mouse over the region of interest, just like you would highlight a sentence in Word. The browser will in on the selected area once you let go of the mouse button.
To retrieve the sequences that were aligned to produce the curves you observe, click one of the curves to select it, then click the I button. If you have pop-up blocking software (external, such as the google toolbar, or built-in, in IE 6 for example), you will need to disable it -- this is usually done by holding down the CTRL key while clicking the button. A new browser window will open that shows details about the alignments in your region. The columns in the display you will see correspond to organisms involved in the alignment. Click on the sequence link to get that organism''s sequence.
Note that short functional elements may not be detected as statistically significant in comparisons of very close species. An extreme example: since the human and chimpanzee genomes are % identical even in neutral regions, the vast majority of exons are too short to stand out as statistically significant in a human-chimpanzee comparison. In general, statistical power to detect short constrained functional elements increases as the total neutral divergence of the compared species increases.
For some reason the default settings in the Opera browser do not grant Java applets printing priviliges. The easiest way to get around this is to save the picture you want as a PDF file and then print it from Acrobat Reader or your favorite PDF viewer. If you are so inclined, however, you can change the Opera configuration files to grant applets printing priviliges and never have to worry about this issue again:
Alternatively, you can click the add curve button. You will see the Add New Curve dialog box. In most cases, selecting the data set you want to see aligned to the base genome is sufficient - just fund it in the drop-down list, and click ok. If you wish, you can change parameters used to calculate the curve and conserved regions, and change the minimum and maximum y-axis values. You can also edit the curve name that describes this curve (this is most useful if you wish to look at two alignments of the same genomes with different calculation parameters).
To add a curve , make sure that the correct base genome is selected in the Base (Reference) Genome menu (please note that changing the base genome will result in switching to that genome, getting rid of any curves that are on the screen at the moment). Use the drop-down menu to select and add a new organism. The counter above the drop-down menu shows how many organisms are available in addition to the ones currently displayed on the screen.
To get annotation for a given segment on the genome, click one of the curves to select it, then click the I button. If you have pop-up blocking software (external, such as the google toolbar, or built-in, in IE 6 for example), you will need to disable it -- this is usually done by holding down the CTRL key while clicking the button. A new browser window will open that shows details about the alignments in your region. Click the Get Annotations in this region link at the top to get a text file containing the annotation.
This panel contains the individual sequences composing the alignment (Fig. 8:8). The panel can be shown only when 655 bases correspond to at least five pixels on the screen, . a small enough region on the base genome. This state is indicated by the appearance of a red rectangle (slider) below the Vista graph (Fig. 8: 7). The slider appears or disappears while in/out. Dragging the slider changes the region displayed on the nucleotide panel.
The Control Panel (Fig. 7) features a drop-down box called Reference (Base) genome, which lists all available base genomes. The current one is selected. Changing the base genome in this box will switch over the whole browser the current curves and annotations will disappear, and the browser will go to the default location on the newly selected genome (see adding curves for more information).
The Vista curve is calculated as a windowed-average identity score for the alignment. A variable sized window (Calc Window) is slid across the alignment and a score is calculated at each base in the coordinate sequence. That is, if the Calc Window is 655 base pairs, then the score for every point X is the percentage of exact matches between the two alignments in a 655bp-wide window centered on that point X. Due to resolution constraints when visualizing large alignments, it is often necessary to condense information about a hundred or more base-pairs into one display pixel. This is done by only graphing the maximal score of all the base pairs covered by that pixel.
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The next field specifies the genome segment displayed by the Browser. To change positions , one can enter specific coordinates on the genome, such as chr9:657,978,676-658,575,779 or contig6585:66657-7786, a gene name , or a contig name. Press the enter key. The browser will go directly to the location of the gene if there is only one exact match, or display a dialog box if there are more than one. Partial gene names are accepted. Please note that the browser does have an upper limit on the size of the region it can display at a time. At this time, it is slightly above 5 million base pairs.
To retrieve the alignments that make up the curves you observe, click one of the curves to select it, then click the "I" button. If you have pop-up blocking software (external, such as the google toolbar, or built-in, in IE 6 for example), you will need to disable it this is usually done by holding down the CTRL key while clicking the button. A new browser window will open that shows details about the alignments in your region. Each alignment that forms a given graph will be shown here, including the overlapped ones. You can get the alignments in mfa format or in a human-readable format by clicking the appropriate links in the right-hand column.
The Nucleotide level panel (Fig. 8: 8) contains two tracks,genome annotations and repeats, which is the same as on the Vista graph panel (see ). The top sequence is the base genome sequence. It is always displayed on the positive strand. Strand directions are indicated by a (+) or (-) sign followed by the organism 8767 s name The name of the base organism is displayed in red. Coordinates on the base genome are drawn above the sequences. Placing a mouse pointer over a nucleotide letter will reveal its coordinate on a genome.
To print a graph, click the Print button. The first time you do this, you will get a dialog box making sure that you indeed requested that something be sent to the printer (Fig. 66). Ths is a security measure in Java intended to handicap malicious code. Click yes. A standard printing dialog box will appear. Proceed like you would with any other printing job. By default, the image will print in landscape (horizontal) layout. Due to Java security measures, changing the layout from the properties box in the print dialog box will not work. If you want to print in portrait (vertical), go to the Curve menu, select Page Setup , and select portrait.
To view the underlying alignments for any curve, click on the curve to select it, then click the Alignment button. If you have pop-up blocking software (external, such as the google toolbar, or built-in, in IE 6 for example), you will need to disable it -- this is usually done by holding down the CTRL key while clicking the button. If you were looking at a region that contained only one alignment, it will be shown to you immediately. If there were several alignments in the region of interest, a window with details about each of the alignments will open, and you will need to select which one you want to look at. Each alignment that forms a given graph will be shown here, including the overlapped ones. You can get the alignments by clicking the appropriate links in the right-hand column.