A Protein Secondary Structure Prediction Server (original) (raw)
Input sequence(?)
Input Sequence Help
JPred requires input as either a single sequence in Raw or FASTA formats (link to format examples) , cut and pasted into the text box. All other formats/options including a multiple sequence alignment or batch submission could be used through advanced options. Show/hide more...
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.
...or upload a file(?)
Upload File Help
Select a plain text file with one or more sequences in a supported file format.
The upload option takes precedence if both inputs have been filled.
Select type of input(?)
Input Format Help
JPred accepts five types of input (link to format examples)
Batch submission of multiple sequences for individual secondary structure prediction could be done using a file in FASTA format (see link to an example above) 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.
Single Sequence (click to select format):
- Raw/Fasta
- Batch Mode
Multiple Alignment (click to select format):
- MSF
- BLC
- Fasta
Skip searching PDB before prediction(?)
Searching the PDB Help
By default JPred searches the PDB before doing a prediction. Show/hide more...
If your sequence has similarity 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.
Check to skip
Email address (optional)(?)
Email Help
Providing an email address means you will be notified of the fate of your job. Show/hide more...
A simple summary of the result will be emailed to you when the prediction is complete. Please make sure your email is valid and correct as the JPred server will not check the validity of it.
Very occasionally we may also use your e-mail address to inform you of changes to the service or major updates.
Query name (optional)(?)
Query Name Help
Provide a name with which to identify your prediction. Show/hide more...
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.
Primary citation: Drozdetskiy A, Cole C, Procter J & Barton GJ. Nucl. Acids Res.
(first published online April 16, 2015) doi: 10.1093/nar/gkv332 [link]
More citations: link.