Release
ProPhylER 1.0 is live now.
News
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
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
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Understanding ProPhylER Search Results
This section is about successful searches. Search failures are discussed here.
Overview
Search by BLAST, Uniprot Accession, Ensembl ID, or PDB ID. When this type of search is successful, ProPhylER provides a Results page.
The Results page will contain several types of links. Clicking on one type of link will launch the ProPhylER Interface; clicking on the other will launch the Crystal Painter. Both are applets that run in browser windows.
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The Interface lets you navigate all the ProPhylER analysis results for the cluster to which your sequence belongs, in sequence/alignment space.
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The Crystal Painter colors a crystal structure with ProPhylER's position-specific estimates of evolutionary constraint. (It uses the Jmol Applet.)
- Depending on how you searched (see below), there may also be a link to a BLAST alignment.
Search by ProPhylER Cluster ID. When this type of search is successful, the Results page only gives a link to an Interface session.
Results Pages
Results pages may be subdivided into an Interface section and a Crystal Painter section, each of which contains the relevant links to the respective sessions.
A. If you did a BLAST search
Your input sequence was Blasted against all sequences in ProPhylER and all current sequences in PDB.
Interface section. ProPhylER ranks the clusters that contain sequences matching your query by their maximum score. The Results page will have links to Interface sessions for the clusters that have matching sequences. Most often there will only be one link to one cluster because matches to multiple clusters are rare. The BLAST alignment link shows the alignment between your query and the best matching ProPhylER sequence. ProPhylER will choose this as the Reference Sequence when you launch the Interface. Sometimes you will be given a choice of reference sequence if there are several equal-scoring matches.
Crystal Painter section. You may also get a link for a Crystal Painter session, if PDB has a crystal structure whose sequence is sufficiently close to your BLAST query. The PBD structure may not exactly correspond to a sequence in your cluster or to your query because of how crystals are made, and how the sequence information is encoded in PDB files. The BLAST alignment link shows the alignment between the sequence ProPhylER found (which will be the reference sequence in the Interface session, and which is not necessarily the same as your query) and the PDB peptide. This is done so you can match up coordinates between the Interface reference sequence and the PDB peptide when you are working simultaneously with Interface and CrystalPainter sessions, as described here.
Note that the Results page gives you at most one link to a Crystal Painter session, but there may be additional PDB files for different crystals, even if they are for the same protein. These are provided as a list with PDB identifiers. If you want a Crystal Painter session with a different crystal for which ProPhylER provided the link, you can repeat the search with that specific PDB ID to get a Crystal Painter link for that exact structure.
B. If you did a Uniprot Accession or Ensembl ID search
The identifier you provided was searched for in ProPhylER.
Interface section. You will get a single link to an Interface session for the cluster that contains the sequence with that ID.
Crystal Painter section. The sequence with the specified ID was retrieved from ProPhylER, and all PDB sequences were Blasted with it. If there was a match, the Crystal Painter and BLAST links will behave exactly as described above in section A.
C. If you did a PDB ID search
A successful PBD ID search means that ProPhylER was able to get the structure file from PDB, parse out the sequences, Blast the ProPhylER sequences with them, and find one or more matching ProPhylER clusters.
Interface section. Depending on how many distinct proteins are in the crystal, ProPhylER will have found one or more matching clusters. Links to Interface sessions with all matching clusters are provided.
Crystal Painter section. Because you searched by a unique PDB ID, there will only be the one relevant link for the Crystal Painter session. The BLAST link has the alignment between the PDB peptide and the best matching ProPhylER sequence.
Last updated 10/05/08