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://supfam.cs.bris.ac.uk/
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SUPERFAMILY database of structural and functional protein annotations for all completely sequenced organisms | supfam.cs.bris.ac.uk Reviews
https://supfam.cs.bris.ac.uk
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.cs.bris.ac.uk
SUPERFAMILY Assignments for Genomes and Sequence Collections
http://supfam.cs.bris.ac.uk/SUPERFAMILY/cgi-bin/gen_list.cgi
Genomic domain assignment statistics. SUPERFAMILY Assignments for Genomes and Sequence Collections. We provide assignments for 3245 distinct organisms. Animals (134), fungi (173), plants (66) and protists (55). Model bacteria (1153) and archaea (121). Animals (5), fungi (46), plants (3) and protists (4);. Bacterial (1442) and archaeal (43). Longest transcript per gene. Eukaryote genomes with splice variants removed. Incomplete, low coverage or early release genomes;. UniProt, PDB, viral sequences etc.
Subscribe/Unsubscribe to the SUPERFAMILY Email List
http://supfam.cs.bris.ac.uk/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.
Genome Names, Identifiers and Phylogenetic Trees
http://supfam.cs.bris.ac.uk/SUPERFAMILY/cgi-bin/genome_names.cgi
Genome names, identifiers and phylogenetic trees. Genome Names, Identifiers and Phylogenetic Trees. Create custom lists of genome identifiers or phylogenetic trees. These lists of genomes can be used to plot phylogenetic trees on this page, or to compare genomes on other pages. Click on the sTOL logo on the right to browse GO terms distributed over the tree. Select a list of genome identifiers. Build a list of comma separated genome identifiers using the genome checkboxes and/or taxon links. Subsp griseu...
EC Hierarchy
http://supfam.cs.bris.ac.uk/SUPERFAMILY/cgi-bin/ec.cgi
Each enzyme is allocated a four-digit EC number, the first three digits of which define the reaction catalysed and the fourth of which is a unique identifier (serial number). Each enzyme is also assigned a systematic name that uniquely defines the reaction catalysed. To navigate hierarchical structure of EC, we display all parental EC terms. To the current EC term of interest ordered by their shortest distances to the current term. Also, only direct children EC terms. Of the current EC term are listed.
SUPERFAMILY database of structural and functional protein annotations for all completely sequenced organisms
http://supfam.cs.bris.ac.uk/SUPERFAMILY/index.html
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.
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Software - Computational Genomics Group
http://www.bioinformatics.bris.ac.uk/software.html
The Mogrify resource predicts how to trans-differentiation from any human cell type to any other human cell typeby perturbing the transcriptional network. Mogrify includes all cell types from the FANTOM5. 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. A community ...
SeqDepot
http://seqdepot.net/stats
Ulrich, L.E. and Zhulin, I.B. Bioinformatics (2014). 8,934,788,107. Transmembrane regions ( DAS. Low complexity regions (seg). Signal peptides ( SignalP. Subcellular locations ( TargetP. Transmembrane regions ( TMHMM. Developed and maintained by Luke Ulrich.
SeqDepot
http://seqdepot.net/download
Ulrich, L.E. and Zhulin, I.B. Bioinformatics (2014). SeqDepot Mongo Database (not currently available for download). Database - all sequences and precomputed features. Excludes all secondary indices (e.g. cross-references). Perl script for performing common tasks. Works with FASTA data or a list of Aseq IDs, GI, UniProt, PDB, or MD5 digests. Produce domain architecture images (PNG or SVG). Easily incorporate into processing pipelines. Encoded data for any (or all) of the following:. Python 3.x module.
Software - Computational Genomics Group
http://www.bioinformatics.bristol.ac.uk/software.html
The Mogrify resource predicts how to trans-differentiation from any human cell type to any other human cell typeby perturbing the transcriptional network. Mogrify includes all cell types from the FANTOM5. 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. A community ...
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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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