No other database than ESTHER holds all alpha/beta hydrolase fold proteins together: Interpro, Prosite, Pfam, have multiple entries for subsets of this structural superfamily. A table Synthese shows the correspondance between these database entries and the subfamilies in ESTHER. The ESTHER Table is now a little to big to be usefull. Each file contains one of the 31219 non redundant proteins/genes. The tables grouped in the family table, the syntheses table or the structure table may be more usefull. The Gene_locus nomenclature for these non-redundant entries is a name with 5 characters for the organisms (3 for genera, 2 for the species, except when a common 5 character name exists. ex: ratno is for Rattus norvegicus and human for man. This allows us to keep close to the Swiss-Prot nomenclature). The last characters define the protein, ex: human-acche represents human acetylcholinesterase. ... [Information of the supplier]
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 2,414 completely sequenced genomes against the hidden Markov models. For each protein you can: a) Submit sequences for SCOP classification; b) View domain organisation, sequence alignments and protein sequence details For each genome you can: a) Examine superfamily assignments, phylogenetic trees, domain organisation lists and networks; b) Check for over- and under-represented superfamilies within a genome For each superfamily you can: a) Inspect SCOP classification, functional annotation, Gene Ontology annotation, InterPro abstract and genome assignments; b) Explore taxonomic distribution of a superfamily across the tree of life All annotation, models and the database dump are freely available for download to everyone. SUPERFAMILY is a member of the InterPro consortium of protein annotation databases, and has been integrated into the Ensembl eukaryotic genome project and The Arabidopsis Information Resource. To date, the SUPERFAMILY publications have been cited over 1,000 times. SUPERFAMILY has been used in structural, functional, evolutionary and phylogenetic research projects. ... [Information of the supplier]
M phase, also called as cell division, is the most crucial and fundamental affair of the eukaryotic cell cycle. After the chromosomes have been replicated during the S phase, the sister chromatids are separated and distributed into two daughter cells equally and faithfully. Also, each daughter cell receives the almost average and necessary intracellular constituents and organelles from the mother cell. Generally, cell division consists of six stages, including prophase, prometaphase, metaphase, anaphase, telophase and cytokinesis. And the first five stages constituent mitosis. During mitosis, numerous proteins organize protein super-complexes at the three distinct regions of centrosome, kinetochore/centromere and cleavage furrow/midbody. Although many proteins have been identified to be localized on centrosome, kinetochore and/or midbody, an integrated resource on this area still remains not to be available. In this work, we have collected all proteins identified to be localized on kinetochore, centrosome, and/or midbody from two fungi (S. cerevisiae and S. pombe) and five animals, including C. elegans, D. melanogaster, X. laevis, M. musculus and H. sapiens. From the related literature of PubMed, numerous proteins have been manually curated to be localized on at least one of the sub-cellular localizations of kinetochore, centrosome and midbody. And to promise the quality of data, based on the rationale of "Seeing is believing", these proteins have been unambiguously observed under fluorescent microscope as directly supportive evidences. Then an integrated and searchable database MiCroKit - Midbody, Centrosome and Kinetochore has been established. The MiCroKit database is the first integrative resource to pin point most of identified components and related scientific information of midbody, centrosome and kinetochore. The version 1.0 of MiCroKit database was set up on Nov. 2nd, 2005, containing 1,065 unique proteins. The MiCroKit version 2.0 was released on Jun. 5th, 2006, with 1,120 entries. Currently, the MiCroKit 3.0 database was updated on July 9, 2009, containing 1,489 unique protein entries. ... [Information of the supplier, modified]
The Mouse Phenome Database (MPD; phenome.jax.org) characterizes strains of laboratory mice to facilitate translational discoveries and to assist in selection of mouse strains for experimental studies. We're a grant-funded research effort headquartered at The Jackson Laboratory. Data sets are voluntarily contributed by researchers from a variety of institutions and settings, or in some cases retrieved by us from open public sources. MPD has three major types of strain-centric data sets: phenotype strain surveys, SNP and variation data, and gene expression strain surveys. See our database stats page for counts and more details. MPD collects data on classical inbred strains as well as any fixed-genotype strains and derivatives that are openly acquirable by community investigators (strain panel examples). Strains can be from JAX-Mice or from any other vendor. Investigators looking to test a diverse set of classical strains should consider our MPD priority strain set. We currently don't subsidize or assist with mouse procurement for projects. ... [Information of the supplier]
The SEQanswers wiki engaging with sequencing and sequencing technology is a Semantic MediWiki (SMW) site that is edited and updated by the members of the SEQanswers community. The wiki provides an extensive catalogue of manually categorized analysis tools, technologies and information about service providers. Within two years, the SEQanswers community has created pages for over 400 unique software tools and associated them with around 350 literature references and 500 web links. SEQwiki contains data for 578 bioinformatics applications, 484 references, and 753 URLs. ... [Information of the supplier, modified]
YeTFaSCo stands for Yeast Transcription Factor Specificity Compendium. It is a collection of all available TF specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats. With it, you can scan sequences with the motifs to find where potential binding sites lie, inspect precomputed genome-wide binding sites, find which TFs have a motif similar to one you have found, and download the collection of motifs. ... [Information of the supplier]
SEVENS summarizes GPCR (G-protein coupled receptor) genes that are identified with high accuracy from 56 eukaryote genomes, by a pipeline integrating such software as a gene finder, a sequence alignment tool, a motif and domain assignment tool, and a transmembrane helix predictor. This treats a larger data space (than that in currently available other databases), which should include not only the expressed sequences but also the newly identified sequences that cannot be detected by in vivo experiments, although they definitely exist on the genome sequence and are just waiting for the opportunity to express their functions. SEVENS can provides the infrastructure of general information of "GPCR universe" for comparative genomics. ... [Information of the supplier]
Bluejay is a set of Java(TM) objects for the processing, display and querying of XML encoded linear scale data. The main subject for analysis in our implementation are genetic and protein sequences, where features fall somewhere on the linear molecules. Bluejay is growing with the goal of creating a graphical genetic data viewer with point-and-click data mining capabilities, such as those available through your standard Web browser. If the image to the left was animated when you first loaded this document, you should have all you need. Otherwise click on the image to obtain the Java Runtime Environment. Please see the publications for more details on Bluejay. ... [Information of the supplier]
The Multi-purpose Automated Genome Project Investigation Environment (MAGPIE, http://magpie.ucalgary.ca/) is a software package for the automated curation and presentation of DNA and protein sequences. MAGPIE distills the results of multiple database searches for each sequence (e.g. expressed sequence tags, ESTs) or subsequence (e.g. open reading frames, ORFs, in bacterial genomic DNA) into a summary page that facilitates interpretation of genes' biological roles and origins. Database search tool used with MAGPIE include the standard NCBI-BLAST set of searches, plus more sensitive Smith-Waterman searches for frameshift prone data such as ESTs. Hidden Markov Model searches are also performed, including against an in-house HMM library derived from the NCBI's Clusters of Orthologuous Genes (COGs) database, including eukaryotic and prokaryotic clusters. HMM searches often provide single, concise, and accurate data for functional assignment. ... [Information of the supplier]
The 2013 IMB Conference will be the first major European meeting to focus on the latest findings and concepts in the fields of chromatin dynamics and stem cells. As such it will bring together experts in epigenetics, developmental biology and cellular reprogramming. The conference will be of interest both to researchers performing basic research in these fields and to applied scientists interested in cellular reprogramming and translational medicine. The conference is open to anyone interested. ... [Information of the supplier]
