Curator Dashboard

Software program for creating montages from multiphoton microscopy.

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• SciCrunch
• 17 years ago - by Anonymous

DroSpeGe provides a preview of newly sequenced Drosophila genomes, with genome maps and BLAST sequence search. Genome maps include D. melanogaster genome homology, homologies to nine eukaryote proteomes, marker gene locations, and Drosophila microsatellites. Current genome assemblies can be BLASTed, with links to genome maps of your BLAST matches. Annotation data are available in Gene Finding Format (GFF) for these whole genome comparisons.

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• SciCrunch
• 17 years ago - by Anonymous

The Stanford Genome Technology Center began a whole genome shotgun sequencing of strain SC5314 of Candida albicans. After reaching its original goal of 1.5X mean coverage of the haploid genome (16Mb) in summer, 1998, Stanford was awarded a supplemental grant to continue sequencing up to a coverage of 10X, performing as much assembly of the sequence as possible, using recognizable genes as nucleation points. Candida albicans is one of the most commonly encountered human pathogens, causing a wide variety of infections ranging from mucosal infections in generally healthy persons to life-threatening systemic infections in individuals with impaired immunity. Oral and esophogeal Candida infections are frequently seen in AIDS patients. Few classes of drugs are effective against these fungal infections, and all of them have limitations with regard to efficacy and side-effects.

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• SciCrunch
• 17 years ago - by Anonymous

An Antibody supplier

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• SciCrunch
• 14 years ago - by Anonymous

Plasma and cell fractions obtained from patients with Diabetes and endocrine diseases and their first degree relatives who agreed to participate in the development of the biorepository. Plasma is aliquoted into multiple specimen containers and stored at -80C. Cell fractions are subjected to DNA and RNA fractionation, aliquoted into multiple specimen containers, and frozen at -70 to -80 degrees centigrade. Anyone who would like to obtain samples from the Biorepository must provide evidence that they have adequate training in the use of bloodborne pathogens, as outlined by OSHA. The investigator must agree to indemnify and hold harmless the Ohio University Diabetes/Endocrine Diseases Biorepository, the Appalachian Rural health Institute, and the Ohio University College of Osteopathic Medicine from any claims, liability, costs, and damages.

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• SciCrunch
• 16 years ago - by Anonymous

The DNA amount in the unreplicated gametic nucleus of an organism is referred to as its C-value, irrespective of the ploidy level of the taxon. The Plant DNA C-values Database currently contains data for 7058 plant species. It combines data from the Angiosperm DNA C-values Database, Gymnosperm DNA C-values Database, the Pteridophyte DNA C-values Database, the Bryophyte DNA C-values Database, together with the addition of the Algae DNA C-values database.

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• SciCrunch
• 16 years ago - by Anonymous

Network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank (PDB). You receive an email notification when the search has finished. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences. Requests can also be submitted by e-mail to dali-server at helsinki dot fi. The body of the e-mail message must contain atomic coordinates in PDB format. If you want to know the structural neighbours of a protein already in the Protein Data Bank (PDB), you can find them in the Dali Database. If you want to superimpose two particular structures, you can do it in the pairwise DaliLite server. Academic users may download the DaliLite program for local use.

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• SciCrunch
• 16 years ago - by Anonymous

It is a database of RNA Junction and Kissing Loop Structures. RNA is versatile in both its structure and function. Within this database you will to able to find more than 12,000 extracted three-dimensional junction and kissing loop structures as well as detailed annotations for each. If you are interested in RNA as a building block for nano-scale design or if you are analyzing the properties of specific RNA motifs you should find utility in this site. The junctions in this database were extracted using a junction scanning algorithm from a number of structures from the Protein Data Bank. Coming from parent structures, both NMR and crystal, these junctions may be under contextual constraints. It is possible that these constraints play a critical role in the junction's conformation and stability.

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• SciCrunch
• 17 years ago - by Anonymous

These programs have been written over the last 20 years for analysis of our own results. They all do some things that are still not available in any commercial program. The programs are written in protected-mode 32-bit Fortran 90, with some assembler subroutines for fast graphics, and the Gino graphics library. Thus they are essentially DOS programs, though they are usually run from Windows, either via a desktop icon (the .ico files) or in the DOS box. The manuals (now in pdf format), have now all been collected into a single document, DCMANUALS.PDF, which should be downloaded, and the bits that you need can then be printed. Note that some sections are common to many or all programs, e.g. the notes on the graph and histogram drawing subroutines, and it is important to read this before using any of the programs (though there is a lot of online help (hit F1) for the graphics, and also in SCAN. Sponsor. Our work was supported by the Wellcome Trust (project grant 074491) and the Medical Research Council (programme grant G0400869).

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• SciCrunch
• 17 years ago - by Anonymous

An Antibody supplier

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• SciCrunch
• 14 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. A relational database in which all editing information such as substitutions, insertions and deletions occurring in a wide range of organisms is stored and maintained in ad hoc designed textual flat files. Individual genes of interest can be searched by appropriate query strings containing the gene name or the intracellular location or the molecular type (as tRNA, rRNA, intron) or the organism or a combination of the previous terms. Moreover, each record of the REDIdb database can be also retrieved according to its specific accession number (more help on how to perform a REDIdb search is available at the ?help? page). To make easier the browsing of each REDIdb entry and quicker the identification of editing sites, two alternative but complementary facilities have been provided either to graphically display genomic and cDNA sequences or to show the corresponding alignment. In both cases, all editing sites are highlighted in colour and their relative positions are shown by mousing over.

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• SciCrunch
• 17 years ago - by Anonymous

A database of motifs found in plant cis-acting regulatory DNA elements, all from previously published reports. It covers vascular plants only. In addition to the motifs originally reported, their variations in other genes or in other plant species reported later are also compiled. The PLACE database also contains a brief description of each motif and relevant literature with PubMed ID numbers. DDBJ/EMBL/GenBank nucleotide sequence databases accession numbers will be also included. Note: As of January 2007, PLACE is no longer updated or maintained.

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• SciCrunch
• 17 years ago - by Anonymous

Software application that is a data mining strategy for detecting and characterizing nonlinear interactions among discrete attributes (e.g. SNPs, smoking, gender, etc.) that are predictive of a discrete outcome (e.g. case-control status). The MDR software combines attribute selection, attribute construction and classification with cross-validation to provide a powerful approach to modeling interactions. (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

Software application based on the Ant Colony Optimization to solve the special case of the traveling salesman problem of ordering markers when the number of loci is large. ANYMAP performs segregation test, linkage grouping and locus ordering, and constructs a linkage map rapidly. (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

Open-source software pipeline for population genomics. Designed for processing genotype and allele data and running population genetic analyses, including conformity to Hardy-Weinberg expectations; tests for balancing or directional selection; estimates of haplotype frequencies and measures and tests of significance for linkage disequilibrium.

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• SciCrunch
• 14 years ago - by Anonymous

Software application to help plan quantitative trait locus (QTL) experiments. (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

The CyberCell database (CCDB) is a comprehensive collection of detailed enzymatic, biological, chemical, genetic, and molecular biological data about E. coli (strain K12, MG1655). It is intended to provide sufficient information and querying capacity for biologists and computer scientists to use computers or detailed mathematical models to simulate all or part of a bacterial cell at a nanoscopic (10-9 m), mesoscopic (10-8 m) and microscopic (10-6 m) level. The CCDB database is actually several databases: CCDB contains quantitative proteomic, genomic and metabolic information about E. coli. CC3D contains 3D structural data for E. coli structural proteomics work CCRD contains detailed information on E. coli RNA molecules CCMD database contains quantitative information on E. coli metabolites. Each database is presented as a re-formattable synoptic table which allows users to casually browse the databases. Detailed information about each gene, protein, RNA, structure or metabolite may be obtained by clicking on the *Card button on the left column. Each card contains more than 60 fields concerning all aspects of the sequence, function or structure of a given molecule. CCDB users may also perform text searches (using the Search button), BLAST sequence searches (using the BLAST button) or conduct more detailed data extraction or relational data searches (using the Extract button).

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• SciCrunch
• 17 years ago - by Anonymous

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