Release
ProPhylER 1.0beta is live now.
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
Ensembl
Uniprot
PDB
WuBlast
Probcons
Semphy
Jmol
Java
Other Links
Sidow Lab
Stanford Pathology Dept
Stanford Genetics Dept
Stanford School of Medicine
Funded by
Help Home Page
Topic Headers are Links to the relevant Help Pages
Hint: Once an Interface or CrystalPainter session is loaded in your browser, all data are on *your* computer. If you keep the window open you will not need to redo the search, or wait for the data to load again.
Searching ProPhylER is quite different from, for example, searching a sequence database by Blast. This page explains how to search ProPhylER effectively, and how ProPhylER searches work.
Because you search ProPhylER with a sequence, but ProPhylER analyses are based on clusters and alignments, your search results may not seem immediately intuitive. This page explains what a search will return and why not all searches give unambiguous results.
You care about *your* protein. But it may not be in ProPhylER, or ProPhylER may not have an analysis for it. Why the $%#& not?? Find out in this section.
If your search was successful and you are presented with the data via the interface, a great deal of information is available to you and you have a number of display choices. This page explains how to navigate the rich ProPhylER analysis space via the interface.
This page explains when, how, and why ProPhylER may have distinct analyses for the same cluster. These analyses are conducted on hierarchically organized subsets of the alignment, encompassing different phylogenetic scopes that may capture distinct information.
The Crystal Painter is ProPhylER's visual display of evolutionary constraint painted right onto a crystal structure (if one is available). This page explains the CP functionality.
This is the grain-of-salt page. ProPhylER's results are predictions, not facts. Learn on this page how to gauge whether the predictions are worth the java code that's used to display them.
Last updated 8/25/08