For a basic search simply input a sequence as a single string and Jpred will make a prediction using default parameters. If you wish to change the defaults then use the 'Advanced' option (see below).
For all searches there is a sequence length limit of 800 residues. Longer sequences should be split into individual domains and searched separately.
Jpred requires input as either a single sequence, cut and pasted into the text box, or a multiple sequence alignment uploaded as a file. It is important not to cut and paste a multiple sequence alignment as the formatting can get messed up. When pasting in a sequence do not add any comment or description lines, but spaces and carriage returns are allowed. You can also upload single sequences as files.
The upload option takes precedence if both inputs have been filled.
Batch submission of multiple sequences for individual secondary structure prediction is now possible via file upload. The file must be in Fasta format and each sequence must be given a unique name (up to 25 characters with no spaces). Additional words or descriptions on the defline will be ignored. Batch jobs cannot be run interactively and results will be provided via e-mail only.
A limit of 200 sequences are allowed per batch submission. You may submit several batch jobs, but there is a hard limit of 4,000 sequence predictions in total per user per day. Please let us know if this limit is a problem for you and we'll look at temporarily changing it.
Searching the PDB
By default Jpred searches the PDB before doing a prediction. If your sequence has homology to a known structure you should reconsider the utility of making a prediction.
The PDB is never searched with alignment or batch queries so this option is ignored for those input types.
Providing an e-mail address means you will be notified of the fate of your job. Plus, a simple summary of the result will be sent to you when the prediction is complete. Please make sure your e-mail is valid and correct as the Jpred server will check the validity of it. Plus, you won't get your results!
Provide a name with which to identify your prediction. If no name is provided a randomly generated one will be used. Query names can only be made up of alphanumeric and '_' characters. Invalid characters will throw up an error. This option is probably not very useful if not used conjunction with an e-mail address.