Alignment Section


ProPhylER shows your protein like you have never seen it before:

Through the lens of Evolutionary Constraint, inferred from
comparative analyses of closely related sequences.

Take a moment to read the overview page, which explains ProPhylER's features, philosophy, and data.

You will find ProPhylER useful if:

Browsers and Operating Systems

We recommend Safari or Firefox on Mac OS X, Firefox or Explorer on PCs. Some versions of 32-bit LInux work, but others, particularly 64-bit, have a range of issues mostly related to Java. Click here for a list of known browser/OS issues and potential solutions.

Start using ProPhylER

The search link on the left is currently the only way to get at ProPhylER data.

Try it out and click on the search link and enter Q75MC9 in the field "Search by Uniprot Accession".

ProPhylER data are displayed with either of two Java applets that you launch in your browser after a successful search: The ProPhylER Interface, which displays data along the sequence of the protein, and the Crystal Painter, which displays evolutionary constraint mapped upon a crystal structure of your protein if one is available.

If you are a first-time user, we recommend the help link on the left (especially the search help).

Understanding some Basics

The documentation link on the left has lots of pages that graphically explain basics of protein evolution.

Your frame of reference is likely a single protein sequence from one organism, but ProPhylER's data are generated by comparative analyses involving lots of homologs. As you explore your protein, bear in mind that the underlying data are evolutionary analyses of a multiple alignment of a cluster of many sequences.

We recommend studying the documentation and making use of the help pages before and during exploration.

Home | Overview | Stats | Search | Help | Documentation | People | Site Map

Last updated 1/11/10


ProPhylER 1.0 is live now.


January 5 2010
The ProPhylER paper is now published in Genome Research

March 12 2010
Searching by name is now supported on the search page

March 12 2010
Searching with hg 18 coordinates for evaluating coding SNPs is now supported


prophyler [at]
arend [at]

Resource Links


Other Links

Sidow Lab
Stanford Pathology Dept
Stanford Genetics Dept
Stanford School of Medicine

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