Standard Mode | Login for job viewer, advanced options and Phyre alarm Retrieve Phyre Job Id
Subscribe to Phyre at Google Groups
Visit Phyre at Google Groups
 Protein Homology/analogY Recognition Engine V 2.0



Overview of running a Phyre2 job

Submitting a job

Running Phyre2 to obtain a model of an amino acid sequence is straightforward. In most cases, all the user has to do is to enter
  • their e-mail address so we can send an e-mail when the job is complete
  • an optional job description
  • The amino acid sequence; Phyre2 will not accept DNA or RNA sequences.
  • Leave the radio button set on "Normal" mode; if you have not used Phyre2 extensively before, Normal mode is what you need.
  • Tell us what type of user you are.

    Very occasionally we will contact commercial users to ask for a letter of support when we are applying for more funding, but otherwise this setting has no effect.

  • A button for submitting the job
phyre2 home page

A note on Intensive mode and why you should not run it

Intensive mode is
  • not "better" than Normal mode except in one rare circumstance.

  • only of use (and even then it is somewhat limited and prone to error) if Normal mode shows that there are multiple models that cover different regions of your sequence. If there is a suitable single model that covers >~60 % of your sequence, the chances that Intensive mode will give a better model are small.

    In a recent examination of results from a plant proteome (240,000 sequences), Phyre2 indicated that 48,000 might benefit from running intensive mode. Of these, ~4,000 would have given a model more than about 40 residues longer than normal mode - so it could be worth running intensive mode for about 1 in 60 sequences.

  • very slow compared to Normal mode; it typically takes 4 - 10 times as long to run a job, and in nearly every case gives the same final answer.

A note on Intensive mode and when you should run it

If the results from normal mode state explicitly that it would be worth running intensive mode, then that is the time to run it. Apart from that specific case, you are probably wasting your time if you do, because normal mode will give you the answer you really want.


After submitting a job

The interface changes and gives you information on the progress of your job;
phyre2 home page phyre2 home page phyre2 home page
if you have entered a non-canonical amino acid, the unacceptable residues are highlighted for normal jobs we give a very rough estimate of how long it might take, but for intensive jobs we don't progress report - there are 5 major steps

On completion

If you have stayed on the page, it will automatically update to the results page when the job has finished. Otherwise, you can follow the link in the results e-mail: Phyre2 results email


Normal run. Top of results page Normal run. Top of results page Intensive run. Top of results page
normal job results the top 20 hidden Markov Models are all modelled by Phyre2 intensive job results

Phyre is now FREE for commercial users!

All images and data generated by Phyre2 are free to use in any publication with acknowledgement

Accessibility Statement
Please cite: The Phyre2 web portal for protein modeling, prediction and analysis
Kelley LA et al. Nature Protocols 10, 845-858 (2015) [paper] [Citation link]
© Structural Bioinformatics Group, Imperial College, London
Michael Sternberg 
Terms and Conditions
Structural Biology Group logo Imperial logo
BBSRC logo
Phyre2 is part of Genome3D