Contents
Gene/Sequence Resources (GSR) serves as a central point for accessing much of the information available at CGD for a 1) a named DNA sequence, 2) a specified chromosomal region, or 3) a raw DNA or protein sequence. This information includes biological information, table/map displays, and sequence analysis and retrieval options. Once you have specified a sequence name or region, GSR will present only those options which are available for obtaining information about your entry.
Whenever possible, selecting one of the available options for your entered sequence name or region takes you directly to the results for your entered sequence. In other cases, it takes you directly to the resource with the sequence already pre-pasted (e.g., BLAST, Restriction Analysis).
Note: Only ONE of the three options listed below may be filled out at a time in order for the submission to be processed.
With this input option, you can enter a gene name, ORF name (e.g., orf19.5007), or a CGDID (e.g., CAL0001571). After you've entered the sequence name, click the "Submit form" button. Note that you can also enter the first few characters of a named DNA sequence followed by the wildcard character (*). Submit the query. Queries that match multiple names will return a list of sequences from which you can then select a single sequence.
You may also retrieve information about flanking sequences upstream and/or downstream of the entered gene/sequence name. To do this, type the length of the flanking region you would like to retrieve in the boxes (upstream and/or downstream) below where you entered the sequence name. Note: negative numbers are not accepted in these boxes. If you would like to retrieve part of an ORF you should use the chromosomal coordinates in retrieval option 2.
If you would like to retrieve or manipulate the reverse complement of the sequence, check the "Use the Reverse Complement" box.
If you decide you would like to change your selection, use the "Reset Form" button found at the bottom of the page to erase your entries.
Select "Submit form" to bring up the list of options available for viewing and retrieving information about the named sequence you entered.
This entry option allows you to specify a region by entering the desired chromosome number and coordinates. To use this option, simply select a chromosome number using the pull-down menu, and then enter the left and right chromosomal basepair coordinates in the boxes provided below. If you do not specify the basepair coordinates, the first 100,000 basepairs will be displayed.
If you would like to retrieve or manipulate the reverse complement of the sequence, check the "Use the Reverse Complement" box. Alternately, enter coordinates in ascending order for the Watson strand and descending order for the Crick strand.
If you decide you would like to change your selection, use the "Reset form" button found at the bottom of the page to erase your entries.
Select "Submit form" to bring up the list of options available for viewing and retrieving information about the named sequence you entered.
This entry option allows you to specify a raw DNA or protein sequence for which you would like to retrieve information. First, use the pull-down menu to select the type of sequence you would like to enter, DNA or protein. Next, position the cursor in the entry box and either type or paste in a sequence.
Note that the sequence entered must be provided in RAW format, without comments (numbers are okay).
If you would like to analyze the reverse complement of the sequence you entered, check the box next to "Use the reverse complement" located below the sequence entry box.
If you decide you would like to change your selection, use the "Reset form" button found at the bottom of the page to erase your entries.
Select "Submit form" to bring up the list of options available for viewing and retrieving information about the named sequence you entered.
After you submit either 1) a named sequence 2) a chromosomal region, or 3) a raw DNA or protein sequence, a page is returned that lists all available information, displays, analyses, and sequence retrieval options available for the sequence. You will choose one of these options. Descriptions for each option are below. Please note that some of them may not be available for your selected entry, depending on the type of sequence you have entered.
If you decide you would like to change your original selection, hit the button [Change Selection or Coordinates]. This will bring back the Gene/Sequence Resources entry page with your information still filled in. You can then modify and re-submit the form.
Availability: This option is available when a gene or ORF name is entered on the Gene/Sequence Resources entry page.
Availability: This option is available when a gene or ORF name is entered on the Gene/Sequence Resources entry page.
Availability: This option is available when a gene or ORF name is entered on the Gene/Sequence Resources entry page.
Availability: This option is available when a gene, ORF, or chromosomal region is entered.
Availability: This option is available when a gene, ORF, or chromosomal region is entered.
Availability: This option is available when a gene name, ORF, chromosomal region, raw DNA sequence, or raw protein sequence is entered on the Gene/Sequence Resources page.
Availability: This option is available when a gene name, ORF, chromosomal region, or raw DNA sequence is entered on the Gene/Sequence Resources page.
Availability: This option is available when a gene name, ORF, chromosomal region, or raw DNA sequence is entered on the Gene/Sequence Resources page.
Availability: This option is available when a gene name, ORF, or chromosomal region is entered on the Gene/Sequence Resources page.
Availability: This option is available when a gene name or ORF is entered on the Gene/Sequence Resources entry page.
Availability: This option is available when a gene or ORF name is entered on the Gene/Sequence Resources entry page.
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