UCSC HMM Applications

(Last Update: 13:19 PDT 13 October 2008 )

SAM-T08

UCSC's SAM-T08 method for iterative SAM HMM construction and remote homology detection and protein structure prediction updates SAM-T06 by incorporating more and better local structure predictions, improved calibration of multi-track HMMs, better contact prediction, and better 3D coordinate prediction. SAM-T08 was tested in CASP8, and produced better results than either SAM-T06 or SAM-T02. It is a good primary server, though metaservers that combine results from many primary servers may still outperform it.

The web page provides a wealth of information, including sequence logos showing relative conservation, sequence logos showing strength of local structure prediction, tables of E-values for fold-recognition results with links to SCOP, alignments to templates, and PDB files with full coordinates.

tiny blue button SAM-T08 alignment, HMM, database query, secondary structure predictions, contact predictions, and 3D structure.
Submit a target protein sequence in FASTA format and receive SAM-T2K, SAM-T04, and SAM-T06 multiple alignments, HMMs, secondary structure predictions, sequence logos, protein database query, pairwise alignments of target to top database hits, contact predictions, and 3D coordinate predictions. This is our current best-performing server.

SAM-T06

UCSC's SAM-T06 method for iterative SAM HMM construction and remote homology detection and protein structure prediction updates SAM-T02 by incorporating newer iterative alignment scripts, more local structure predictions, improved multi-track HMMs, contact prediction, and full 3D coordinate prediction. SAM-T06 was tested in CASP7, and produced better results than either SAM-T99 or SAM-T02. It is a good primary server, though metaservers that combine results from many primary servers outperform it.

The web page provides a wealth of information, including sequence logos showing relative conservation, sequence logos showing strength of local structure prediction, tables of E-values for fold-recognition results with links to SCOP, alignments to templates, and PDB files with full coordinates.

tiny blue button SAM-T06 alignment, HMM, database query, secondary structure predictions, contact predictions, and 3D structure.
Submit a target protein sequence in FASTA format and receive SAM-T2K and SAM-T04 multiple alignments, HMMs, secondary structure predictions, sequence logos, protein database query, pairwise alignments of target to top database hits, contact predictions, and 3D coordinate predictions.

SAM-T02

UCSC's SAM-T02 method for iterative SAM HMM construction and remote homology detection and protein structure prediction updates SAM-T99 by using predicted secondary structure information in its scoring functions. Both SAM-T99 and SAM-T02 were "server" entries to CASP5, CASP6, and CASP7.
tiny blue button SAM-T02 alignment, HMM, database query, secondary structure predictions and more
Submit a target protein sequence in FASTA format and receive SAM-T02 alignment, HMM, protein database query, secondary structure predictions, sequence logos and pairwise alignments of target to top database hits.
tiny blue button Yeast protein predictions
We have pre-computed SAM-T02 predictions for all the ORFs of S. cerervisiae, and created a web page similar to the results returned by the SAM-T02 server. The web pages are not currently indexed---to find a protein like YBL008W you have to go to the subdirectory YBL0/YBL008W and get the summary.html file. We update some of the yeast predictions each month, based on new structures released in PDB.

SAM-T99

UCSC's SAM-T99 method for iterative SAM HMM construction and remote homology detection and protein structure prediction updates the earlier SAM-T98 method and adds new capabilities. This method will be our "automatic" entry to CASP-4, though we will use more experimental methods for our "hand" entry.
tiny blue button SAM-T99 alignment, HMM, protein database query, and secondary structure prediction (SERVICE DISCONTINUED)
Submit a protein sequence (or alignment) in FASTA format and receive SAM-T99 alignment, HMM, database hits, and secondary structure prediction. This site has been mostly superseded by the SAM-T02 site, but we'll keep it running as long as we can, since several meta-servers use it. We urge anyone doing new work to use the SAM-T02 server instead.
tiny blue button SAM-T99 Model Libary Search (SERVICE DISCONTINUED)
Submit a protein sequence in FASTA format and receive hits from UCSC's SAM-T99 protein structure HMM library.
tiny blue button SAM-T99 alignment tuneup (SERVICE DISCONTINUED)
Align a set of protein sequences or refine an existing multiple alignment.
tiny blue button SAM DNA and RNA alignment tuneup (SERVICE DISCONTINUED)
Align a set of DNA (or RNA) sequences or refine an existing multiple alignment.
tiny blue button SCOP superfamily search and alignment library.
This official SCOP site now provides SAM-T99 models for searching the SCOP database. These models and the underlying alignments were created with the SAM tools, but not here at UCSC.
tiny blue button SAM-T99 FAQ
Frequently asked questions about SAM and the SAM-T99 web site.

SAM-T98

The SAM-T98 server is obsolete. It should not be used for any new work.


   Email sam-info@soe.ucsc.edu with questions and problems
   UCSC Computational Biology Group
   SAM Home Page
  

(Last Update: 13:19 PDT 13 October 2008 )

Page originally designed by Jeffrey Sukharev, jsukhare@soe.ucsc.edu, now maintained by Kevin Karplus karplus@soe.ucsc.edu