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A database on composite regulatory elements affecting gene transcription in eukaryotes. Composite regulatory elements consist of two closely situated binding sites for distinct transcription factors, and provide cross-coupling of different signalling pathways.TRANSCompel was created by a commercial entity, but is usable by the academic community on a limited bases for free. Composite regulatory elements are found in many promoters and enhancers of eukaryotic genes. They consist of two binding sites of two different transcription factors, which through this combination form a module with new regulatory properties. Composite elements frequently serve as integration sites of two (or more) signaling pathways.TRANSCompel is equipped with our proprietary CATCH program, an analysis software for searching potential composite elements in DNA sequences. A sequence under study is scanned by this program using all composite elements collected in TRANSCompel as individual searching patterns. All found matches are directly linked to the TRANSCompel entries containing the corresponding composite elements.

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• SciCrunch
• 17 years ago - by Anonymous

A marker database designed to provide experimental details and useful marker information allelotyped in Taiwanese populations accompanied by resources and technical supports. Our aims to construct TPMD are to share useful genotyping information including data of genotyped microsatellite markers, genotyping resources and laboratory supports for promoting genotyping and gene cloning of prevalent diseases. TPMD contains microsatellite markers with di-, tri-, and tetranucleotide repeats deposited by four qualified genotyping laboratories and presented with user-friendly web interfaces for researchers. The newly developed TPMD graphic displays with integration of markers into genetic, cytogenetic and physical maps not only show the comparison of marker’s heterozygosities in Taiwanese, Japanese, and Caucasian but also facilitate the selection and download of commonly used microsatellite markers for refined mapping and positional candidate cloning of disease genes.

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• SciCrunch
• 17 years ago - by Anonymous

Collection of transmembrane protein datasets containing experimentally derived topology information from the literature and from public databases. Web interface of TOPDB includes tools for searching, relational querying and data browsing, visualisation tools for topology data.

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• SciCrunch
• 17 years ago - by Anonymous

This database functions both as a website where researchers can look for information on their targets of interest; and as a tool for prioritization of targets in whole genomes. Using the database as a tool, researchers can quickly prioritize a genome of interest by performing any number of individual queries on a species of interest, then assigning numerical weights to each query (in the history page) to finally obtain a ranked list of genes by combining the weighted queries. This site is part of a WHO/TDR project seeking to exploit the availability of diverse datasets to facilitate the identification and prioritization of drug targets in pathogens causing neglected diseases.

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• SciCrunch
• 14 years ago - by Anonymous

The taxonomically broad EST database TBestDB serves as a repository for EST data from a wide range of eukaryotes, many of which have previously not been thoroughly investigated. Users can search by annotated name, EC#, and view datasets that contain classification hierarchies for pathways, for reactions (the enzyme nomenclature system), for compounds, and for genes. Most of the data contained in TBestDB has been generated by the labs of the Protist EST Program located in six universities across Canada.

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• SciCrunch
• 17 years ago - by Anonymous

TassDB stores extensive data about alternative splice events at GYNGYN donors and NAGNAG acceptors. Currently, 114,554 tandem splice sites of eight species are contained in the database, 5,209 of which have EST/mRNA evidence for alternative splicing. Users can search by Transcript Accession Number and Gene Symbol, SQL Query, and Tandem Donor/Tandem Acceptor pairs.

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• SciCrunch
• 17 years ago - by Anonymous

TargetDB, a target registration database, provides information on the experimental progress and status of targets selected for structure determination. Search sequences from the PSI Structural Genomics Centers and other Structural Genomics projects.For more information about how these proteins were cloned, expressed, purified, or other experimental protocols please go to the Protein expression, purification, and crystallization DataBase.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 26,2019. In October 2016, T1DBase has merged with its sister site ImmunoBase (https://immunobase.org). Documented on March 2020, ImmunoBase ownership has been transferred to Open Targets (https://www.opentargets.org). Results for all studies can be explored using Open Targets Genetics (https://genetics.opentargets.org). Database focused on genetics and genomics of type 1 diabetes susceptibility providing a curated and integrated set of datasets and tools, across multiple species, to support and promote research in this area. The current data scope includes annotated genomic sequences for suspected T1D susceptibility regions; genetic data; microarray data; and global datasets, generally from the literature, that are useful for genetics and systems biology studies. The site also includes software tools for analyzing the data.

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• SciCrunch
• 13 years ago - by Anonymous

SYSTOMONAS is a comprehensive database of molecular networks in Pseudomonas focusing on Pseudomonas aeruginosa. We use a systems biology approach to get a deeper understanding of all cellular processes of P. aeruginosa during infection. Our long term goal is the development of a dynamic model simulating P. aeruginosa during infection. The basis for such an approach is SYSTOMONAS, a comprehensive database that includes systems data from all levels of analysis as microarray and proteomics data, metabolite measurements, sequence data, gene-regulatory networks and enzyme data. Therefore, we started with metabolomics analysis and extended to transcriptomics, genomics, and proteomics aspects. Along with the wet lab results additional data is stored, which is extracted from literature or derived from other external databases. Major sources of SYSTOMONAS are KEGG, PRODORIC, BRENDA (see section ''Sources''), which are partly stored via the data warehouse system and partly dynamically connected via SOAP, a platform-independent data transfer protocol. Comparing a Pseudomonas protein of interest with other well-characterized proteins may deliver useful insights into the evolution, distribution, and species specific function. Therefore, we searched for all deduced proteins of the SYSTOMONAS database for orthologous proteins in other Pseudomonas species to obtain orthologous protein clusters. Pseudomonas aeruginosa, systems biology, transcriptomics, genomics, proteomics

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• SciCrunch
• 17 years ago - by Anonymous

This is a dataset of clinical HIV sequences, including a method of decoding the evolutionary pathways by which HIV evolves drug resistance. "Fitness landscape" describing how HIV proteins can evolve, is shown as a kinetic network. Drug resistance is a major problem in the treatment of AIDS, due to the very high mutation rate of human immunodeficiency virus (HIV) and subsequent rapid development of resistance to new drugs. Identification of mutations associated with drug resistance is critical for both individualized treatment selection and new drug design. We have performed an automated mutation analysis of HIV Type 1 (HIV-1) protease and reverse transcriptase (RT) from approximately 50,000 AIDS patient plasma samples sequenced by Specialty Laboratories Inc. from 1999 to mid-2002. This dataset provides a nearly complete mutagenesis of HIV protease and enables the calculation of statistically significant Ka/Ks values for each individual amino acid mutation in protease and RT. Positive selection (i.e., Ka/Ks>1 indicating increased reproductive fitness) detected 19 of 23 known drug-resistant mutation positions in protease and 20 of 34 such positions in RT. We also discovered 163 new amino acid mutations in HIV protease and RT that are strong candidates for drug resistance or fitness. Our results match available independent data on protease mutations associated with specific drug treatments and mutations with positive reproductive fitness, with high statistical significance (the P values for the observed matches to occur by random chance are 1e-5.2 and 1e-16.6, respectively). Our data indicate that positive selection mapping is an analysis that can yield powerful insights from high-throughput sequencing of rapidly mutating pathogens. This database has been made possible by the generous contribution of HIV sequence chromatograms by Specialty Laboratories, Inc.

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• SciCrunch
• 17 years ago - by Anonymous

Software for a de novo exact match tandem repeat finder which main advantage is without the need to specify either the pattern or a particular pattern size, integrated with a data visualization tool and has a built-in user-friendly Graphical User Interface.

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• SciCrunch
• 13 years ago - by Anonymous

SYSTERS is a database of protein sequences grouped into homologous families and superfamilies. The SYSTERS project aims to provide a meaningful partitioning of the whole protein sequence space by a fully automatic procedure. A refined two-step algorithm assigns each protein to a family and a superfamily. The sequence data underlying SYSTERS release 4 now comprise several protein sequence databases derived from completely sequenced genomes (ENSEMBL, TAIR, SGD and GeneDB), in addition to the comprehensive Swiss-Prot/TrEMBL databases. To augment the automatically derived results, information from external databases like Pfam and Gene Ontology are added to the web server. Furthermore, users can retrieve pre-processed analyses of families like multiple alignments and phylogenetic trees. New query options comprise a batch retrieval tool for functional inference about families based on automatic keyword extraction from sequence annotations. A new access point, PhyloMatrix, allows the retrieval of phylogenetic profiles of SYSTERS families across organisms with completely sequenced genomes. Gene, Human, Vertebrate, Genome, Human ORFs

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• SciCrunch
• 17 years ago - by Anonymous

A database ofhuman disease-related mutated proteins identified by mass-spectrometry (MS). For achieving this goal, we collected human mutated sequences known to be related to diseases till now. After surveying mutated sequence sources: PMD, OMIM, SwissProt polymorphism, HGMD, etc, we found that currently HGMD contains the largest human gene mutation information. However, because, for academic users, HGMD does not provide with whole data download service, we decided to systematically extract and curate mutation information from PMD, OMIM, SwissProt, MSIPI database to form SysPIMP and provide it free for academic users.

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• SciCrunch
• 17 years ago - by Anonymous

A database containing the results of a large-scale protein annotation and local structural comparison project. A non-redundant set of protein chains is used to build a database of protein surface patches, defined as putative surface functional sites. Each patch is annotated with sequence and structure-derived information about function or interaction abilities. Users can search the annotations and the results of the surface patches comparisons stored in the DB based on PDB code, PROSITE pattern, or ligand. A new procedure for structure comparison is used to exert an all-versus-all patches comparison. Selection of the results obtained with stringent parameters offers a similarity score that can be used to associate different patches and may allow reliable annotation by similarity. protein, protein structure, structural comparison, protein ligand, protein surface, protein morphology

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• SciCrunch
• 17 years ago - by Anonymous

SUPERFAMILY is a database of structural and functional protein annotations for all completely sequenced organisms. 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 1,700 completely sequenced genomes against the hidden Markov models.

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• SciCrunch
• 17 years ago - by Anonymous

Software for identifying haplogroups from low coverage sequence data.

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• SciCrunch
• 13 years ago - by Anonymous

Subtilist is a database dedicated to the analysis of the genome of Bacillus subtilis. It provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments. It also allows one to easily browse through these data and retrieve information, using various criteria (gene names, location, keywords, etc.). The purpose of the website is to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria. The data contained in SubtiList originated mainly from the worldwide collaborative B. subtilis genome sequencing project, supplemented with information from the B. subtilis entries present in the EMBL/GenBank/DDBJ databanks, as well as observations either published in international journals or communicated directly to us by individual researchers.

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• SciCrunch
• 17 years ago - by Anonymous

Software that predicts microsatellites with Tandem Repeats Finder (TRF).

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• SciCrunch
• 13 years ago - by Anonymous

StrainInfo.net connects users with information resources on different strains and taxa of microorganisms. The StrainInfo.net bioportal was established to stimulate movement towards the use of multi-perspective integrated information in a broadened biological and clinical context. It brings together the biological material kept at multiple biological resource centers into a single portal interface, with direct pointers to the relevant information at the collections'' websites, and provides both historical traces and geographic distribution of the strains they keep in culture. In addition, this information is automatically linked to related sequences in the public domain and refers to all known scientific publications that deal with the organism. To support taxonomic depth of the information provided by the StrainInfo.net bioportal, all taxonomic names appearing in the bioportal are fully integrated with and linked out to key taxonomic information sources. Predefined workflows allow further integration of additional information sources into the bioportal, resulting in direct access to all organisms involved in completed or ongoing whole-genome sequencing projects. As the bioportal further unfolds itself as a helpful add-on to the microbiologists'' toolbox, we hope to gather around it a growing community of users that might become active contributors to both its content and implementation.

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• SciCrunch
• 17 years ago - by Anonymous

Database to explore known and predicted interactions of chemicals and proteins. It integrates information about interactions from metabolic pathways, crystal structures, binding experiments and drug-target relationships. Inferred information from phenotypic effects, text mining and chemical structure similarity is used to predict relations between chemicals. STITCH further allows exploring the network of chemical relations, also in the context of associated binding proteins. Each proposed interaction can be traced back to the original data sources. The database contains interaction information for over 68,000 different chemicals, including 2200 drugs, and connects them to 1.5 million genes across 373 genomes and their interactions contained in the STRING database.

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• SciCrunch
• 17 years ago - by Anonymous