Intro
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Submit PseudoKnot

PseudoBase is a collection of RNA pseudoknots we make available for retrieval to the scientific community.

This page enables you to submit a pseudoknot. If you want to help us and submit a pseudoknot we appreciate your contribution.

To help you enter pseudoknot data each item has a small explanation (hover over the info-button) and an example. For more information, please consult AboutPseudoBase. Alternatively you can consult the publication about this database (see Batenburg et al. (2000)).

Please make sure first that the pseudoknot you submit is not yet in the database (see database).


Your email is needed for questions we may have about your input. If you do not want your email included in pseudobase you can indicate so in the check-box below the email-field. If you do not enter anything in the email-field, the program will assume that you are a web-robot and your information is not submitted (if you really want to be anonymous you can fill in a bogus email; even "@" will suffice).
Also, don't forget to cross the appropriate box under caption "supported by:".

Submission form

Enter a description of the location of the pseudoknot.
Definition:
example:
Enter the name of the organism whose rna contains the pseudoknot.
Organism:
example:
Enter the abbreviation of the virus/pseudoknot.
Abbreviation:
example:
Characterise the type of RNA containing the pseudoknot.
We have pre-defined a number of types that we think may be useful as an rough classification.
RNA type:
example:
Enter a few words that characterize the pseudoknot.
Keywords:
example:
Enter here access code of the sequence in the EMBL-database in Heidelberg (http://www.ebi.ac.uk/).
EMBL Accession number:
example:
Enter your name here.
Submitted by:
example:
Enter your email so we can contact you if we have any questions about the submitted data. If you really want to be anonymous, you can enter a bogus-email; if you leave this empty the program assumes you are a web-bot.
Email address:
example:
Check this if you want to give us the opportunity to contact you in case we have any questions about your submission, but you do not want your email recorded in PseudoBase.
Email consent:
Do NOT put my email in PseudoBase.
example:
Do NOT put my email in PseudoBase.
Enter here the fragment of the nucleotide sequence that contains the pseudoknot.
First enter the sequence number of the first nucleotide followed by blanc (no return!),
next enter the nucleotides of the sequence fragment in caps followed by blanc (no return!),
finally enter the sequence number of the last nucleotide.
Pseudoknot sequence:
example:
Enter here the positions of stems S1 and S2.
For bulges and internal loops you enter all stemparts.
Positions paired:
example:
Please mention here by what type of research the pseudoknot is supported.
We only accept data from pseudoknots that are (published and) supported by experimental data.
Supported by:
Crystal structure
Mutagenesis
NMR
Sequence comparison
Structure probing
Others:
example:
Crystal structure
Mutagenesis
NMR
Sequence comparison
Structure probing
Others:
Enter the literature reference(s) of the publication that describes this pseudoknot. See example for layout.
We only accept data from pseudoknots that are published (and supported by experimental data).
Reference:
example:
Enter here any comment that is useful to know for this pseudoknot.
For a message to the PseudoBase manager (that's me, yes), please do not use this field but send me an email ("Contact"-line at bottom-left of this page).
Comment:
example:


Contact:
Prototyping: Jacky Ng & Jan Oliehoek.
Final design and maintenance: Eke van Batenburg; 1998-3-10;...;