LAGAN -- global pair-wise and multiple alignment of finished sequences. If some of the sequences are in a draft format your query will be redirected to AVID to obtain multiple - pairwise alignment. Multiple alignment will be visualized by VISTA that will calculate and display sequence conservation projected on any sequence you indicate as a base. This is the only alignment program available through this server that produces true multiple alignments.
It detects rearrangements and inversions in sequences while producing a global end-to end map. If you input several sequences all pair-wise combinations will be processed and results visualized in VISTA. This is the only alignment program available through this server that can detect rearrangements and inversions.
Select names for your species that will be shown in the legend. We suggest that you use something meaningful, such as the name of an organism, the number of your experiment, or your database identifier. When you use a GenBank identifier to input your sequence, by default we will use it as a name of the sequence. If a gene annotation of the sequence is available you can submit it in a simple plain text format to be displayed on the plot.
Each gene is defined by its start and end coordinates on the sequence, and the name listed on one line. The exons are listed individually with the word "exon", after the start and end coordinates of each exon. UTRs are annotated the same way exons, with the word "utr" replacing "exon".
There is an easy way to export annotations in the above format from the Ensembl genome browser. Here is how it can be done:. Our web server also accepts annotations in GFF3 format. We recommend masking a base sequence to get better alignment results.
You can submit either masked or unmasked sequences. We also accept softmasked sequences, where repetitive elements are shown as low-case letters while the rest of the sequence is shown in capital letters. In this case you need to select "softmasked" option in the menu.
If your sequences are unmasked, our server will mask repeats with RepeatMasker. Please select a specific mask for your base sequence in the menu. Select the alignments for which you want to reverse-complement second sequence try this if you get no homology when you expect to see it.
Several minutes after submitting your sequences you will receive email from vista lbl. Below is the results page. During the course of Java plugin detection, it is sometimes necessary to insert one or more Java applets into the web page, and then to query those applets. The JavaAppletObj property gives you access to one of these applets.
All the properties of the PluginDetect. This is a Java security feature which some users may find to be annoying. PluginDetect has no control over this popup. So consider carefully before using the getDeploymentToolkitObj method. Returns null if no attempt was made to detect the Toolkit. Thus it is unknown whether the Toolkit is installed or not. The purpose of this array is to detect multiple JREs. The version strings are in the exact same format used by the Deployment Toolkit plugin ie.
This is only for non-Internet Explorer browsers. Can be a string such as '1,5,0,0' or '1. Can be a number such as 0 or 1. If minVersion is not specified, then PluginDetect will assume minVersion is '0'. Strings are more versatile than numbers since '1,5,0,1' cannot be expressed as a number. Even though it is an optional input, it is strongly recommended that you use the jarfile input argument when doing Java detection.
Otherwise a number of Java cases will not be detectable. The jarfile path can be relative or absolute. If the path is relative, then it is relative to the web page itself, not relative to any external javascript file you may be using. The getJavaInfo. You are free to rename the getJavaInfo. The verifyTagsArray is optional and usually does not need to be set by the user.
The result of this detection is given by INFO. This parameter is only used by Internet Explorer. The verifyTagsArray is discussed in more detail later on. The event handler has been called. Run displayResults when Java detection done. Of course, you are free to specify the jarfile in all your PluginDetect methods if you wish. But to do so would be redundant. If your jarfile path is relative, then it is always relative to the web page itself.
For example, if the getJavaInfo. If the getJavaInfo. The easiest way to do this is to go to the PluginDetect download page , select the "Java" option, select the "verify jarfile" option, and then press the "Create Script" button. The resulting script should then be used in your Java detection web page.
The verifyTagsArray input argument We previously mentioned that when PluginDetect tries to detect Java, it will start out by using the non-applet detection methods. If the non-applet methods fail to detect anything, then PluginDetect resorts to using the applet detection methods ie.
Java applets. The applets are inserted into your web page using HTML tags. The applets are queried to determine the Java version, and then they are deleted from the page. There are 3 applet detection methods.
And INFO. The verifyTagsArray which is an optional input argument determines when these 3 applet methods are to be used for Java detection. The array contains 3 numbers:. The numbers in verifyTagsArray can be 0, 1, 2, 2. For instance, the array could be [1,1,1] or [0,1,2] or [3,3,3] or [3,1,1] or whatever. If the user does not specify a value for the array, then PluginDetect assumes a default value.
This default is sufficient for most users. You therefore do not even need to bother with setting verifyTagsArray at all. We now give a few examples of what happens with different values of verifyTagsArray :. None of the applet methods will ever be used. If it succeeds in detecting the Java version, then we are done.
PluginDetect will only wait long enough for results from any one of the applets, though it is possible most likely that results for all 3 are obtained.
Either way, PluginDetect will try to get detection results for all 3 tags. The other 2 applet methods are never used. Note: if you want to verify that the path and filename of jarfile 'getJavaInfo.
This will force the jarfile to be used with the applet detection methods. After that, you can return verifyTagsArray to whatever value you want. If you do not give any value to verifyTagsArray , then it a default value is used. This default value is usually sufficient for most detection needs. We now show the specific HTML tags that are used for each of the applet detection methods Once this Java applet has been inserted into the page, the applet is queried to see if the Java version can be detected.
The applet is deleted from the document after detection has been completed. The verifyObjectTag parameter determines if and when this method may be used for Java detection. The verifyAppletTag parameter determines if and when this method may be used for Java detection. The verifyObjectTagActiveX parameter determines if and when this method may be used for Java detection.
The verifyTagsArray input argument appears right after the jarfile input argument. Since jarfile only needs to be specified in the very first PluginDetect method that runs, you would therefore only need to specify verifyTagsArray in that first PluginDetect method.
For example, we could have:. You have complete flexibility in what values you wish to assign to the array. Or, you could choose to not specify any value at all. The array then goes to it's default value. Omicron is bad news. Wear masks. Avoid crowds. Ventilate if you can. Rapid test if available. We have the tools. We must use them. SELF does not provide medical advice, diagnosis, or treatment. Any information published on this website or by this brand is not intended as a substitute for medical advice, and you should not take any action before consulting with a healthcare professional.
Colleen Stinchcombe grew up in the deserts of California and Arizona before transplanting herself to the Pacific Northwest.
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