The Burnham Institute
Bioinformatics Server
FFAS03		A new, updated and maintained version of the Fold & Function Assignment System (FFAS). The FFAS fold assignment method is based on the profile-profile matching algorithm. The crucial part of the algorithm is the novel, two dimensional weighting scheme which takes into account the topology of the evolutionary tree of all the proteins in the homologous family. User registration required. This service is not available to commercial users.
FATCAT		Pairwise flexible protein structure alignment server. See Y. Ye and A.Godzik "Flexible structure alignment by chaining aligned fragment pairs allowing twists" Bioinformatics, 2003, 19(Suppl 2):II246-II255 for details.
POSA		Multiple flexible protein structure alignment server. See Y. Ye and A.Godzik "Multiple flexible structure alignment using partial order graphs" Bioinformatics, 2005 21(10):2362-2369 for details
JAFA		JAFA provides clear, concise annotation to protein sequences. The Joined Assembly of Function Annotations, a function annotation meta-server, accepts a protein sequence, and queries several function prediction programs. The programs' results are assembled and reported as Gene Ontology terms, with links to the original predictions, a graphic description, and XML files so that JAFA can be incorporated into your own work-flow.
CADO		Comparative Analysis of protein Domain Organization. A graph theory method to survey and compare domain organization across genomes. Described in Genome Research, 2004, 14:343-353
Fragnostic		Mapping the Protein Structure Universe using Recurring Structural Fragments. A graph theory method to survey inter-fold similarities. Described in an upcoming manuscript in Journal of Molecular Biology
SEA		A novel approach to protein sequence alignment, the structure SEgment Alignment (SEA) is based on the network mathcing approach, and profile-profile comparison of short fragments of sequence. See Y. Ye, W. Li, L. Jaroszewski, and A. Godzik "A Segment Alignment Approach to Protein Comparison" Bioinformatics, 2003, 19:742-9 for details.
FRAGlib		This server predicts local structure segments in proteins by the profile-profile matching algorithm based on the database of short (7-19aa) secondary structural motifs chosen from ASTRAL SCOP database.
Pacgum		Pacgum is a tool for checking the regularity of atomic packing in any given 3D model of protein. It discriminates low-resolution from high-resolution protein structures and uses a purely geometric approach which is independent from the origin of the model.
Wikiomics		Wikiomics is a wiki for the bioinformatics community that is hosted on one of our servers. The principle is to reduce the communication barriers between scientists, by letting anyone instantly edit, review, update and discuss any part of the web site. Hosted under an independent domain name, we are confident Wikiomics will become a tool of choice for every modern scientist concerned with bioinformatics.
Retired Servers (not updated since 2001, only accessible inside of Burnham Institute)
PDB Blast		PDB database search with PSI-Blast using a profile generated from NR data base. Such a narrowing of the search scope was shown to improve the effectiveness of NR database search.
Web Modeller		Web Modeller is a web server with user-friendly interface, which assists users to do comparative homology modeling using the Modeller package.
Genomes		Genomes is a database containing fold assignments and preliminary function assignments for proteins from three microbial genomes: E.coli, M.genitalium and H.pylori, as described in our papers (see the publication list)
BIFFAS		Blast initiated FFAS (BIFFAS): the version of FFAS method where the initial sequence profile is not calculated automatically but is generated by hand. This allows customization of the profile which is then used for the search in the clustered PDB database. In order to get into BIFFAS, one uses the FFAS login page.
Benchmarks		The comparison of fold & function assignment strategies with comprehensive benchmark.