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This database contains different yeast strains searchable by ORF and gene name, and serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The database is hyperlinked with other public databases. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function. 5791 heterozygous diploid and 4706 homozygous diploid deletion strains were monitored in parallel using molecular barcodes on fermentable (YPD, YPDGE) and non-fermentable substrates (YPG, YPE, YPL). The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition. Strains can be searched by ORF or Gene name to access growth measurements and data plots for each strain. Category: Genomics Databases (non-vertebrate) Subcategory: Fungal genome databases Category: Organelle databases Subcategory: Mitochondrial genes and proteins

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. A relational database that contains all the eukaryotic protein-encoding DNA sequences in GenBank. It provides detailed and comprehensive features about both the intron containing and the intron-less genes. In addition to the information found in the GenBank records, which includes properties such as sequence, position, length and description about introns, exons and protein coding regions, Xpro provides annotations on the splice sites motifs and intron phases. Furthermore, Xpro validates intron positions using alignment information between the records sequence and EST sequences found in dbEST. The entries in the XPro are also cross-referenced to SWISS-PROT/TrEMBL and Pfam databases. Unprecedented growth data in GenBank, the primary repository of nucleotide sequences due to the ever increasing number of genome and EST sequencing projects and the poor annotation of exon/intron details required for molecular evolution studies in the primary nucleotide database have made development of Xpro database. It is a specialized database that contains details about genomic features specific to eukaryotic genes and provides various web tools for analyzing/visualizing these features., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 08, 2011. The VNTRDB is a database useful for searching common polymorphic tandem repeats or unique tandem repeats in selected bacteria. Additionally, a visualization tool is accompanied with this database to observe sequence differences between bacterial strains and to avoid false positive records result from misestimating copy number and locus length of tandem repeats. Variable number tandem repeats (VNTRs) are one kind of DNA markers that have been widely used in molecular typing of bacteria. For finding potentially polymorphic tandem repeats, more genome sequences of a bacterial species should be compared. Till now, however, only 357 bacterial genome sequences are fully sequenced. Many of these bacterial species merely one strain has been sequenced. Therefore, all fully sequenced bacteria of a same genus are usually compared together to find the polymorphic potency of tandem repeats. It means that the more bacteria or sequences are compared, the more polymorphic tandem repeats will be truly identified. Here, a variable number tandem repeat locus database (VNTRDB) was constructed to microbiologists to meet the requirements of epidemiological studies. All potentially polymorphic tandem repeats in this database are found by comparing homologous tandem repeat loci between different bacteria of a same genus or among different genera. Currently, we provide two kinds of tandem repeats for query in the VNTRDB, i.e., polymorphic TRs and putatively unique TRs. These two query pages contain their own setting parameters for searching common polymorphic tandem repeats or unique tandem repeats in selected bacteria. This VNTRDB is an open resource and can be freely accessed without any restriction. The data in it will be updated or added continuously when new bacterial genome sequences are fully sequenced. Category: Genomics Databases (non-vertebrate) Subcategory: Prokaryotic genome databases

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• SciCrunch
• 17 years ago - by Anonymous

GenePath is a web-enabled intelligent assistant for the analysis of genetic data and for discovery of genetic networks. GenePath uses abductive inference to elucidate network constraints and logic to derive consistent networks. Typically, it starts with a set of genetic experiments, uses a set of embedded rules (patterns) to infer relations between genes and outcome, and based on these relations constructs a genetic network.

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• SciCrunch
• 17 years ago - by Anonymous

Resource for experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Most of these noncoding elements were selected for testing based on their extreme conservation in other vertebrates or epigenomic evidence (ChIP-Seq) of putative enhancer marks. Central public database of experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Users can retrieve elements near single genes of interest, search for enhancers that target reporter gene expression to particular tissue, or download entire collections of enhancers with defined tissue specificity or conservation depth.

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• SciCrunch
• 17 years ago - by Anonymous

This interdisciplinary Neuroscience Program is one division of the Biomedical Sciences Graduate Program at the University of New Mexico. Participating faculty are affiliated with the Department of Neurosciences. Students complete a core curriculum in biomedical sciences and then an individualized program of courses and research in neuroscience. Students may choose among neuroscience research laboratories in the Neurosciences Department or at the Los Alamos National Laboratories. Neuroscience graduate students are part of an active neuroscience group that sponsors weekly seminars and journal clubs.

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• SciCrunch
• 17 years ago - by Anonymous

A database containing predicted viral miRNA candidate hairpins. Users may query the putative miRNA hairpins of a specific viral species by the hierarchical menu or by search function using the GenBank Identifier or RefSeq accession number. In addition, users can also search for the putative target genes of a particular viral miRNA hairpins by a RNAhybrid service link. We have previously identified human intronic microRNA as well as zebrafish microRNA. The microRNA hairpin discovery pipeline was also applied to discover viral encoded microRNAs. All viral genomes were obtain from NCBI. The classification of virus is based on the taxonomy table of NCBI (Jun, 2006). Totally, the genomes of 2266 viruses were analyzed. The 3’-UTR regions of human, mouse, rat, zebrafish, arabidopsis and rice genes are available for search.

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• SciCrunch
• 17 years ago - by Anonymous

A database for icosahedral virus capsid structures. The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration. Users can find links to the PDB coordinates of virus structures, rendered structural images of viral subunits, capsids, and crystal contacts, as well as find basic information such as family, genus, and number of subunits of different viruses. Viperdb includes powerful search utilities, links to other relevant databases, background information on virus capsid structure, and useful database interface tools. It describes various icosahedral virus capsid structures in the Protein Data Bank (PDB) in terms of their complete capsids, detailed structural and computational analysis. Additionally, all virus capsids are placed in a single icosahedral orientation convention, facilitating comparison between different structures. The protomeric (asymmetric unit) coordinates were transformed and stored in a single icosahedral convention (2(Z)-3-5-(X)2). Coordinates (sometimes) were further processed by rearranging the nucleic acid residues, hetero atoms, and water molecules (if present) at the end of the protein chains for the ease of further analysis. Structures are classified in terms of their quasi-symmetry (e.g. T=3, T=4, T=7) and pseudo-symmetry (e.g., P=3).Tools are being developed to study the capsids in terms of structural, energetic and assembly aspects . The derived results are made available throught this website. The site is being developed as part of the training, service and dissemination component of the NIH Research Resource: Multiscale Modeling Tools for Structural Biology (MMTSB).

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• SciCrunch
• 17 years ago - by Anonymous

An integrated and comprehensive database of virulence factors for bacterial pathogens (also including Chlamydia and Mycoplasma). VFDB is a platform for further study of comparative pathogenomics. Major features include tabular comparison of pathogenomic composition in terms of virulence, multiple alignments and statistic analysis of homologous virulence genes, and graphical comparison of pathogenomic organization of VFs. Category: Genomics Databases (non-vertebrate) Subcategory: Prokaryotic genome databases

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• SciCrunch
• 17 years ago - by Anonymous

This is a database of microsatellite sequences (short tandem repeats useful in gene comparison and kinship studies) present in 80 genomes. Users can search the database by microsatellite type, repeat unit length (mono- to hexa-nucleotide), repeat number, microsatellite length and repeat sequence class. They can also search by specifying EST, cDNA, CDS identity or by using Gene Index, GenBank, UniGene IDs. Microsatellites, also known as simple sequence repeats (SSRs) or simple tandem repeats (STRs), have extensively been exploited as molecular markers for diverse applications including genome characterization and mapping. Recently, their role in gene regulation and genome evolution has also been discussed widely. We have developed UgMicroSatdb (Unigene MicroSatellite database), a web based relational database of microsatellites present in unigene sequences covering 80 genomes. UgMicroSatdb allows microsatellite search using multiple parameters like microsatellite type simple (perfect) and compound (perfect and imperfect), repeat unit length (mono- to hexa-nucleotide), repeat number, microsatellite length and repeat sequence class. Microsatellites can also be retrieved by specifying EST, cDNA, CDS identity or by using Gene Index, GenBank, UniGene IDs. The database also provides information about trinucleotide repeats encoding various amino acids. Such codon repeats can be searched by specifying characteristics of coded amino acids like charge (basic, acidic or neutral), polarity (polar or non-polar) and their hydrophobic or hydrophilic nature. The nucleotide sequences of the target UniGenes are also provided to facilitate primer designing for PCR amplification of any desired microsatellite.

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• SciCrunch
• 17 years ago - by Anonymous

A Biological Proteome KnowledgeBase linking IPI and SPTR-NR based Proteome analyses with TranScout, TransMem and ProtLoc and offering crosslinks with other relevant information from worldwide highly acknowledged biodatabases such as SWISS-PROT, NCBI Refseq, Ensembl, InterPro or Gene Ontology Annotation. TrSDB is a BioDB (Biological Relational DataBase) that through the same web interface joins several predictive analyses of protein motifs, domains, cellular localization and functional annotation around different compiled sequences, now IPI and SPTR Non-Redundant proteomes.TranScout, TransMem and ProtLoc predictions with crosslinks to InterPro, Gene Ontology Annotation, ENSEMBL, SWISS-PROT/TREMBL, REFSEQ and inter and intraspecies precomputed BLAST Analyses are provided when suitable for each proteome entry. By now, nine eukaryotic organisms proteomes (human, mouse, rat fruit fly, worm, Arabidopis, an alga and two yeasts) may be queried. Periodically compiled proteomes will be updated all at the same time to mantain temporal coherency and new analyses will be provided as well.When one organism has been selected, a funny icon in the upper-right part of the web screen may help you to remind your organism selection.Emphasis is placed upon Transcription Factor prediction supported by TranScout. Complex analyses are performed searching for Transcription Factor evidence from TranScout and InterPro matches as well as existing GO annotation. Mutual transcription factor evidence among homologues is also considered and compiled analyses files are available.

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• SciCrunch
• 17 years ago - by Anonymous

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
• 14 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