SUPERFAMILY database of structural and functional protein annotations for all completely sequenced organisms. Protein annotations are based on a library of Hidden Markov Models built from the expertly curated SCOP (Structural Classification of Proteins) database.
http://www.supfam.org/
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SUPERFAMILY database of structural and functional protein annotations for all completely sequenced organisms | supfam.org Reviews
https://supfam.org
SUPERFAMILY database of structural and functional protein annotations for all completely sequenced organisms. Protein annotations are based on a library of Hidden Markov Models built from the expertly curated SCOP (Structural Classification of Proteins) database.
supfam.org
Subscribe/Unsubscribe to the SUPERFAMILY Email List
http://www.supfam.org/SUPERFAMILY/maillist.html
Email list subscription options. Subscribe/Unsubscribe to the SUPERFAMILY Email List. This low traffic mailing list provides notification of major SUPERFAMILY releases and updates. You can expect a few emails per year. We do not share, sell or rent your personal information to third parties - ever. Enter email address to add or remove. Follow us on twitter. Please send feedback, comments or questions to superfamily@cs.bris.ac.uk. Or use the feedback form.
Download SUPERFAMILY Models, Database Dump and Genome Assignments
http://www.supfam.org/SUPERFAMILY/downloads.html
Download SUPERFAMILY Models, Database Dump and Genome Assignments. Seed sequences for models. Amazon EC2 AWS image. It is no longer necessary to install SUPERFAMILY locally. Instead you may use our EC2 AWS cloud image. To gain access to downloads from the SUPERFAMILY server a license agreement. Must be obtained, which is free for academic and commercial use. There is a short registration. The hidden Markov models are available for download in HMMER3 (/models/hmmlib 1.75.gz) format in the models d...There...
SUPERFAMILY Sitemap
http://www.supfam.org/SUPERFAMILY/sitemap.html
Sitemap showing the main SUPERFAMILY pages. Taxonomic ordering of genomes. Genome names and their identifiers. Adjacent domain pair lists and graphs. Domain combinations in groups of genomes. Taxonomic visualisation of domain combinations. How to use the models. A2m to selex script. Amazon EC2 AWS cloud image. Representation of a superfamily. How to use the MySQL database. How to use the hidden Markov models. Setup models and scripts. Use scripts to produce domain assignments. Or use the feedback form.
dcGO - A comprehensive domain-centric ontology resource for post-genomic research on functions, phenotypes, diseases and more
http://www.supfam.org/SUPERFAMILY/dcGO
DcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more. What is dcGO ( Background. As a biomedical ontology resource, dcGO integrates knowledge from a variety of contexts, ranging from functional information like G. Ntology (GO) to others on enzymes and pathways, from phenotype information across major model organisms to information about human diseases and drugs. In dcGO, all B. Ntologies that are not GO are collectively referred to as BO. How dcGO is built ( Algorithm.
Home @ supraHex 1.7.3
http://www.supfam.org/supraHex
SupraHex 1.7.3. An open-source R/Bioconductor package for tabular omics data analysis using. The artwork called supraHex. Has won The Best Artwork Award in ISMB 2014. This artwork is automatically done and is reproducible here. Demonstrated in a variety of genome-wide datasets such as:. And clonal population structure. Is a giant hexagon on a 2-dimensional map grid seamlessly consisting of smaller hexagons. For more, see slides. And poster in ISMB2014. Visualisations at and across nodes of the map;.
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FANTOM
http://fantom2.gsc.riken.go.jp/fantom2/doc/links.html
Computational analyses and curation. FANTOM cDNA annotation system (CAS). T Kasukawa et al. in preparation. Web-based system for human curation of sequences. T Kasukawa et al. in preparation. Displays seqencing quality (PHRED) scores. M Furuno et al. in preparation. Graphical viewer that shows homologous regions to protein sequences and start/stop condons for each frame. J Adachi et al. in preparation. RIKEN cDNA sequence clustering, viewer, and editor. RIKEN expression array database. FASTY is a program...
Disorder
http://www.d2p2.pro/about/predictors
Details on the predictors included in the database, both protein structure and disorder. Algorithm authorship is stated where necessary, as well as a contact details for all data providers. Search Instead ». This page contains brief descriptions of the predictors included in the D. If you have any specific comments or issues with a given predictors assignments a point of contact for that data provision is linked. For more general enquiries or comments please contact Matt Oates. Li,X, Romero,P. Genome Inf...
About - Database
http://www.d2p2.pro/about/database
Search Now ». Please cite the following if you make use of D. As well as papers for any original prediction methods used. Oates,M.E., Romero,P., Ishida,T., Ghalwash,M., Mizianty,M.J., Xue,B., Dosztányi,S., Uversky,V.N., Obradovic,Z., Kurgan,L., Dunker,A.K., Gough,J. (2013). "D2P2: Database of Disordered Protein Predictions.". D1):D508-D516 DOI: 10.1093/nar/gks1226. Website, and database analysis. VLXT and VSL2b predictions. Espritz and IUPred-L predictions. VLXT and VSL2b predictions.
Resource: SUPERFAMILY
http://www.genome3d.eu/resource/id/SUPERFAMILY
CATH / SCOP Mapping. Laquo; Back to all resources. The SUPERFAMILY database provides SCOP structural domain annotation of protein sequences at the superfamily and family levels using a library of HMMs. Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. Lewis TE and Sillitoe I,. Nucleic Acids Res. 2013 Jan;41(Database issue):D499-507. Prof Sir Tom L Blundell (FUGUE). Prof Cyrus Chothia (SCOP). Prof Julian Gough (SUPERFAMILY).
PROSITE links
http://prosite.expasy.org/prosite_link.html
Databases of protein domains and families. Pattern and profile searches. Databases of protein domains and families. Database of protein families and domains. The universal protein resource (includes UniProtKB, UniRef, UniParc). Links to related databases and portals. UniProtKB family classification and annotation. Portal to human UniProtKB/Swiss-Prot variants implied in diseases. Portal to viral UniProtKB/Swiss-Prot entries. Chordata (includes human) Protein Annotation Program. Database of protein famili...
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supfaceee (Kayla) - DeviantArt
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SUPERFAMILY database of structural and functional protein annotations for all completely sequenced organisms
SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes. The SUPERFAMILY annotation is based on a collection of hidden Markov models. Which represent structural protein domains at the SCOP. Superfamily level. A superfamily groups together domains which have an evolutionary relationship. The annotation is produced by scanning protein sequences from over 2,478 completely sequenced genomes. Against the hidden Markov models. Submit sequences for SCOP classification.
SUPFAM database
Evolutionary relationships between structure and sequence families. How to use the site. This database consists of clusters of potentially related homologous protein domain families, with and without three-dimensional structural information, forming superfamilies. The present release (Release 6.0) of SUPFAM uses homologous families in Pfam (Version 27.0) and SCOP (version 1.75) which are examples of sequence -alignment and structure classification databases respectively. New Features of SUPFAM web-site.
SUPERFAMILY database of structural and functional protein annotations for all completely sequenced organisms
SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes. The SUPERFAMILY annotation is based on a collection of hidden Markov models. Which represent structural protein domains at the SCOP. Superfamily level. A superfamily groups together domains which have an evolutionary relationship. The annotation is produced by scanning protein sequences from over 2,478 completely sequenced genomes. Against the hidden Markov models. Submit sequences for SCOP classification.
SUPERFAMILY database of structural and functional protein annotations for all completely sequenced organisms
SUPERFAMILY is currently undergoing maintenence. We will be back very soon, please check again later. Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure.". Please send feedback, comments or questions to superfamily@cs.bris.ac.uk.
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