Curator Dashboard

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1, 2023. Cardviews is a CARDinal plane VIEWing System developed at the Center for Morphometric Analysis at the Massachusetts General Hospital. It is a tool for brain morphometry (including volumetric analysis using xvol) and this program emerged as a product of our methodological development. While some of its functionality is specifically tailored for our general segmentation and neocortical parcellation routines, the imaging interface, segmentation tools, and localization capacity have utility extending beyond the specific aims motivating its initial conception. :

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• SciCrunch
• 17 years ago - by Anonymous

The Chloroplast Genome Database contains annotated chloroplast/plastid genomes from the NCBI Organelle Genomes section at NCBI. Users can search for genes by their annotated names, conduct flexible BLAST searches, download protein and nucleotide sequences extracted from a selected chloroplast genome, and browse the putative protein families (tribes) created using TribeMCL.

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• SciCrunch
• 17 years ago - by Anonymous

The CutDB focuses on the annotation of individual proteolytic events, both actual and predicted. Its offers searchable lists of proteases, Merops code, substrate, and diseases from which users can specify their desired queries in order to obtain more specific information. CutDB is one of the first systematic efforts to build an easily accessible collection of documented proteolytic events for natural proteins in vivo or in vitro. A CutDB entry is defined by a unique combination of these three attributes: protease, protein substrate and cleavage site. Currently, CutDB integrates 3070 proteolytic events for 470 different proteases captured from public archives (such as MEROPS and HPRD) and publications. CutDB supports various types of data searches and displays, including clickable network diagrams. Most importantly, CutDB is a community annotation resource based on a Wikipedia approach, providing a convenient user interface to input new data online. A recent contribution of 568 proteolytic events by several experts in the field of matrix metallopeptidases suggests that this approach will significantly accelerate the development of CutDB content.

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• SciCrunch
• 17 years ago - by Anonymous

The database of germline p53 mutations is a comprehensive database covering all published cases of germline p53 mutations. The current version lists 580 tumors in 448 individuals belonging to 122 independent pedigrees. The database describes each p53 mutation (type of the mutation, exon and codon affected by the mutation, nucleotide and amino acid change), each family (family history of cancer, diagnosis of Li-Fraumeni syndrome), each affected individual (sex, generation, p53 status, from which parent the mutation was inherited) and each tumour (type, age of onset, p53 status-loss of heterozygosity, immunostaining). Each entry contains the original reference(s).

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• SciCrunch
• 17 years ago - by Anonymous

DBAli is a database that includes a comprehensive all-against-all comparison of protein structures in the PDB database. It is not currently being updated; however, updates should resume in the near future. All pairwise structural comparisons in DBAli have been obtained using the MAMMOTH program developed in the group of Prof. Angel R. Ortiz. All multiple structure alignments in DBAli have been obtained using the SALIGN command in MODELLER developed in the group of Prof. Andrej Sali.

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• SciCrunch
• 17 years ago - by Anonymous

DomIns is a web resource aimed at providing comprehensive information on domain insertions in proteins of known structure. We have followed the definition of protein domains as in the SCOP (Structural Classification of Proteins) database in order to identify insertions. We have considered only the major five classes (All-alpha, All-beta, alpha/beta, alpha+beta and Small Proteins), the fold and the superfamily level of SCOP hierarchy for identifying insertions. Apart from browsing insertions in whole PDB, we also provide an option to browse insertions in a pre-computed list of non-redundant PDB chains provided by PDB_Select with a sequence identity threshold of 90%.

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• SciCrunch
• 17 years ago - by Anonymous

SAPALDIA (Swiss study on Air Pollution and Lung Disease in adults) is a multi-center study in eight geographic areas representing the range of environmental, meteorological and socio-demographic conditions of Switzerland, which studies the effects of air pollution on the respiratory and cardiovascular health in adults. Local centers are: Aarau, Basel, Davos, Geneva, Lugano, Montana, Payerne, and Wald. It was initiated in 1991 (SAPALDIA 1) with a follow-up assessment in 2002 (SAPALDIA 2). This study has allowed to assess 1) prevalence and development of major respiratory and allergic symptoms and diseases and the age-related decline in lung function, 2) the distribution of heart rate variability in the general population over age 50, 3) the association of these health indicators with individual long term exposure to air pollution, other toxic inhalants, life style and molecular factors. Another follow-up examination (SAPALDIA 3) started in January 2010. This study is well positioned to address crucial questions of air pollution epidemiology and important environmental health policy-related questions in the coming years. When SAPALDIA was initiated in 1991, 9''''651 subjects, aged 18 to 60 years, were recruited for a detailed computer-based interview and more than 90% of them underwent lung function and atopy testing. More than 7''''000 of the subjects had bronchial reactivity tested by a methacholine challenge. SAPALDIA shares parts of its study protocol with the European Community Respiratory Health Survey (ECRHS) with which it is linked through the study center of Basel. Since 1991 SAPALDIA has been carefully following address histories of its participants. In the 2002 follow-up, 8''''047 (83%) provided health information, 6''''528 persons underwent physical re-examination, and 6''''345 provided blood samples to establish an extensive blood, plasma, serum and DNA bank. In addition, 1''''813 subjects aged 50 or older participated in 24h-ECG Holter monitoring to provide detailed data on parameters of heart rate variability. With the inclusion of cardiovascular endpoints, SAPALDIA is one of the first studies examining effects from long-term exposure to air pollution on cardiovascular health parameters as well as mutual influence between the respiratory and the cardiovascular system. The SAPALDIA bio-bank has allowed scientific publications on the association between some genetic profiles (gene polymorphism) and the propensity to develop asthma, allergic diseases, or accelerated lung function decline with age. Ongoing studies are focusing on gene-environment interactions a crucial question to understand why some persons suffer more from the effect of air pollution than others.

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• SciCrunch
• 15 years ago - by Anonymous

An Antibody supplier

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• 14 years ago - by Anonymous

An Antibody supplier

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• 14 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. eQTL Explorer was developed as a computational resource to visualize and explore data from combined genome-wide expression and linkage studies is essential for the development of testable hypotheses. This visualization tool stores expression profiles, linkage data and information from external sources in a relational database and enables simultaneous visualization and intuitive interpretation of the combined data via a Java graphical interface. eQTL Explorer also provides a new and powerful tool to interrogate these very large and complex datasets. eQTLexplorer allows users to mine and understand data from a repository of genetical genomics experiments. It will graphically display eQTL information based on a certain number of selection criteria, including: tissue type, p-value, cis/trans, probeset Affymetrix id and PQTL type. Sponsors: This work was funded by the MRC Clinical Sciences Centre and the Wellcome Trust programme for Cardiovascular Functional Genomics.

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• SciCrunch
• 17 years ago - by Anonymous

The MIPS Fusarium graminearum Genome Database aims to present information on the molecular structure and functional network of the entirely sequenced, filamentous fungus Fusarium graminearum (Anamorph of Gibberella zeae). The goal is to provide a comprehensive genome database in the Genome Research Environment in parallel with other fungal genomes to enable in depth fungal comparative analysis. The underlying sequence is the initial release of the high quality draft sequence of the Whitehead Center for Genome Research.

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• SciCrunch
• 17 years ago - by Anonymous

An Antibody supplier

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• 14 years ago - by Anonymous

This is a searchable database of U12-type introns. U12-type introns are spliced by the U12-dependent spliceosome and are present in the genomes of many higher eukaryotic lineages including plants, chordates and some invertebrates. Investigations into the evolution and mechanism of U12-depending splicing would be facilitated by access to a catalog of such introns. However, due to their relatively recent discovery and a systematic bias against recognition of non-canonical splice sites in general, the introns defined by U12-type splice sites are under-represented in genome annotations. Such under-representation compounds the already difficult problem of determining gene structures. It also impedes attempts to study these introns genome-wide or phylum-wide. The resource described here, the U12 Intron Database (U12DB), aims to catalog the U12 introns of completely sequenced eukaryotic genomes and associate orthologous introns with each other.Two pathways for the removal of eukaryotic spliceosomal introns exist: a major pathway that is dependent on the main U2 snRNA-containing spliceosome and a minor pathway that is dependent on the low abundance U12 snRNA-containing spliceosome. The two spliceosomes share only one snRNA, U5, but have many of the same protein components in common. They are distinguished mainly by the splice signal sequences in the pre-mRNA to which they bind. U12 consensus sequences for the donor site, RTATCCTTT, and branch point, TTCCTTRAY, are highly conserved and distinct from the U2 consensi. The two spliceosomes also differ in the order of spliceosomal assembly. U11 and U12 form a dimer which then recognizes the donor site and branch point simultaneously, whereas U1 and U2 recognize these sites independently before associating.Computational scans for U12 introns have previously been performed for human (Levine and Durbin, 2001) and Arabidopsis (Zhu and Brendel, 2003). Both scans used similar methodology, essentially predicting introns and confirming them using alignment to expressed sequence. We extended this approach to 20 genomes using spliced alignment of sequence flanking known introns or transcript-confirmed intron predictions to the genomic sequence of orthologous genes. Details can be found in forthcoming article in the Nucleic Acids Research database issue.

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• SciCrunch
• 17 years ago - by Anonymous

A stand-alone package to identify and analyze conserved k-mers in pairwise alignment. This program shows high performance for identifying miRNA seed binding sites in 3''-UTRs.

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• SciCrunch
• 16 years ago - by Anonymous

It is part of the Institute for Advanced Studies at The Australian National University (ANU). CBiS forms a bridge between two areas of major strength at ANU, mathematics and biological sciences. CBiS brings together researchers with backgrounds in mathematics, statistics and quantitative biology with the goal of developing a conceptual architecture for an information-based, integrative approach to complex biological systems. Software available for download or use is: * Pozitiv * GE Bi-Plot * Chip Stability * PyEvolve * Vestige Most software is freely available under the GPL or similar licenses. For details, see each individual package., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 14 years ago - by Anonymous

A database listing potential G-quadruplex regulated genes. G-rich DNA sequences can form G-quadruplexes, a four-stranded structure that is stabilized by planar arrays of four guanines associated with hydrogen bonds. Promoter G-quadruplexes have emerged as a new way to regulate gene transcription, such as in c-MYC expression. Further, G-quadruplex motifs are highly enriched in gene promoter regions in humans and other mammals. Greglist contains genes whose promoter regions have G-quadruplex motifs, and these genes are highly likely to be regulated by G-quadruplexes.

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• SciCrunch
• 17 years ago - by Anonymous

Organization which manufactures bacteria for research and clinical investigations. List Biological Laboratories cultivates native and recombinant microorganisms and purifies, formulates, and lyopholizes enzyme products, virulence factors, and microbial cell wall components. Products include antibodies, microbial toxins, peptides, and virulence factors. Services include live biotherapeutics for clinical trials, contracting research capabilities, GMP regulatory support, lyopholization services and support, and toxin compliance.

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• SciCrunch
• 14 years ago - by Anonymous

An Antibody supplier

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• 14 years ago - by Anonymous

IVDB hosts complete genome sequences of influenza A virus generated by BGI and curates all other published influenza virus sequences after expert annotations. For the convenience of efficient data utilization, our Q-Filter system classifies and ranks all nucleotide sequences into 7 categories according to sequence content and integrity. IVDB provides a series of tools and viewers for analyzing the viral genomes, genes, genetic polymorphisms and phylogenetic relationships comparatively. A searching system is developed for users to retrieve a combination of different data types by setting various search options. To facilitate analysis of the global viral transmission and evolution, the IV Sequence Distribution Tool (IVDT) is developed to display worldwide geographic distribution of the viral genotypes and to couple genomic data with epidemiological data. The BLAST, multiple sequence alignment tools and phylogenetic analysis tools were integrated for online data analysis. Furthermore, IVDB offers instant access to the pre-computed alignments and polymorphism analysis of influenza virus genes and proteins and presents the results by SNP distribution plots and minor allele distributions. IVDB aims to be a powerful information resource and an analysis workbench for scientists working on IV genetics, evolution, diagnostics, vaccine development, and drug design.

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• SciCrunch
• 17 years ago - by Anonymous

A non-supervised gene prediction algorithm for prokaryotic genomes with multivariate entropy distance method.

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• SciCrunch
• 13 years ago - by Anonymous