Welcome!
You may find ProPhylER useful if:
- You conduct structure-function studies on eukaryotic proteins
- You have missense SNPs in eukaryotic protein-coding genes
- You want to find functionally important regions in your protein
- You want to explore your protein from a new perspective ... that
may in fact be a billion years old
Take a moment to read the OVERVIEW page, which explains ProPhylER in detail.
Browsers and Operating Systems
We recommend Safari or Firefox on Mac OS X, Firefox or Explorer on PCs. We cannot recommend LInux because of a range of issues mostly related to Java.
Start using ProPhylER
The SEARCH link on the left is currently the only way to get at ProPhylER data.
If you are a first-time user, we recommend the HELP link on the left (especially the search help).
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.
Loading speed may be an issue. We do not know how much demand we will have and how our server will handle the load. Please be patient if loading data takes a while.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.
Last updated 10/05/08
Release
ProPhylER 1.0beta will be Live on Thursday, Oct 9.
News
ProPhylER 1.0 is a beta release with all functionality implemented except browsing by name.
Contacts
prophyler [at] prophyler.org
arend [at] stanford.edu
Resource Links
Java (needed for this site)
Ensembl
Uniprot
WuBlast
Probcons
Semphy
Jmol
Other Links
Sidow Lab
Stanford Pathology Dept
Stanford Genetics Dept
Stanford School of Medicine
Funded by
