Uploading Reference Sequences



Reference sequences are the sequences against which other sequences are aligned and determine the scope of chromatogram that is displayed in the chromatogram view.

Note: Only group SuperUsers and Administrators are able to upload or modify reference sequences, however, once this is done, they will be visible to all users within that user group.

Adding new sequences
When a new usergroup is created, WebRECall does not provide any standard reference sequences for you. All must be provided by the user.

Creating a sequence from scratch
Creating a new sequence is the easiest way to obtain a new reference sequence. Take your pre-existing reference sequence, a section from HXB2 genome for example, paste it into WebRECall and it will store the sequence for you indefinitely. Plain-text formatting is required.

To add a reference sequence to the list, follow the following steps:

 Select &lt;new sequence&gt; from the list Replace the Name label with the label you desire for your reference; Keep in mind: Reference sequences must possess unique names. Paste the sequence into the large text box Press the Create button 

Note: '-' representing deleted characters are permitted, as are the nucleotide mixture characters: BDHVRYKMSW and N. All other characters will result in the reference sequence being rejected. Currently U is not supported. ERROR: [Invalid nucleotide sequence]

Creating a reference sequence subsection
If you would rather use only part of one of your existing reference sequences, it is possible to designate a subsection of the sequence using the 'Base Range' fields. The first field indicates the nucleotide upon which the subsection will begin, and the second field indicates where the subsection should end.

The first nucleotide in a sequence is designated 1.

As the fields are completed, a blue selection area will appear in the text area, highlighting the area of interest.

Once you have verified that your subsection is correct, give your sequence a new name in the Name field, and press the Create button. Your new reference subsection will appear in the sequence list.

Changing the name / ID of a reference sequence
Highlight the reference sequence you would like to rename. Adjust the spelling of the name in the Name field and press the Update button. The reference sequence will be renamed.

Changing the sequence of a reference
Highlight the reference sequence you would like to adjust, and modify the sequence that appears in the text box on the right. Once your modifications are complete, press the Update button.

Deleting a sequence
Simply highlight the reference sequence ID from the Sequence List and press the Delete button.