SUPERFAMILY
The SUPERFAMILY database contains assignments of protein domains of known structures to all completely sequenced genomes. The library of hidden Markov models and the software required to run the SUPERFAMILY assignment procedure is available from the downloads page. There is a very low traffic mailing list for notification of updates/changes.
Domain-centric Gene Ontology
dcGO is a domain-centric solution to function prediction and functional genomics. Gene Ontology terms have been mapped to SUPERFAMILY domains, supra-domains and architectures. The method has been assessed for its ability to predict GO terms on sequences in the CAFA competition. This dcGO also contains Phenotype Ontology terms and Anatomy ontology terms mapped from 8 different ontologies.
Database of disordered protein predictions
D2P2 A community resource for pre-computed disorder predictions over a large library of known amino sequence. Goals of the database include making statistical comparisons of the various prediction methods freely available to the prediction community. As well as facilitating biological investigation of the disordered protein space.
Database of disordered protein predictions
Spiricoil is a website for Coiled Coil prediction in sequences. It also includes the option to view detected coiled coils mapped on known structures and even generate 3D models and view them. Spiricoil also includes the assignment of Coiled Coils to all completely sequenced genomes.
SNP/SNV functional and phenotypic analysis
The Functional Analysis Through Hidden Markov Models (FATHMM) software and server is capable of predicting the functional and phenotypic consequences of protein missense variants using hidden Markov models (HMMs) representing the alignment of homologous sequences and conserved protein domains.
Vector Graphics tree plotting
TreeVector is a utility to create and integrate phylogenetic trees as Scalable Vector Graphics (SVG) files. One of the main purposes of TreeVector is to move away from treating phylogenetic trees as end end point and final graphic, and to instead embed them in dynamic processes using web standard technologies, so that quick reference of a particular pattern or trait is possible, dynamic and up to date.
HMM profile-profile comparison
This was the work of Martin Madera whilst in the group. He wrote PRC the PRofile Comparer. It is a stand-alone program for aligning and scoring two profile hidden Markov models, but can also handle PSI-BLAST profiles.