Dataset submission
The usage of our tools is extremely simple. When a new submission is desired, user is presented with following simple form (screenshot):
The form has following components:
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Basic information
Run title and email address. Both are optional, however, the email address needs to be either empty or filled in and valid. Arbitrary text in the email field will prevent submission. Providing an email address to receive the notification of job completion is optional but strongly suggested when submitting multiple sequences.
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Input data
A dataset with RNA sequences in FASTA format either by pasting them in the text area (maximum 25000 characters allowed) or by uploading a file. The user can incorporate modified nucleotides such as inosine (I), pseudouridine (P), dihydrouridine (D), m6A (6), 7DA (7), and nebularine (9) by replacing the desired nucleotides with I, P, D, 6, 7, and 9, respectively.
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Organism Selection
The algorithm exploits a series of pre-calculated proteome reference datasets derived from the following species that could be employed in the computation of the interactions.
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Transcript Fragmentation
The user can decide to fragment the RNA or keep it unfragmented. We recommend a window of 100 nucleotides around the modified nucleotide to best assess the effect on the interactions.
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Submission status
This field is periodically updated and informs user about the status of the submission. The submit button is inactive until all of the required information is provided.