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motif-x (short for motif extractor) is a software tool designed to extract overrepresented patterns from any sequence data set. The algorithm is an iterative strategy which builds successive motifs through comparison to a dynamic statistical background.

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• SciCrunch
• 17 years ago - by Anonymous

Service center in Stanford School of Medicine providing genomics services:High-throughput Sequencing (Illumina), Library Generation for Illumina High-throughput Sequencing,Microarray Gene Expression (Affymetrix, Agilent, Illumina),QC for RNA, DNA, and High-throughput Sequencing Libraries,Whole Genome Genotyping (Illumina),Real-time PCR, gene expression, genotyping, melt, etc.Sample Preps,DNA and RNA extractions, Plasmid preps, NanoString, Microarrays and Microarray Printing, Access to Instrumentation and Software. Supports all arrays based on microscope format including Agilent, Illumina, Nimblegen, and arrays produced by SFGF. Besides printing cDNA and oligonucliotide microarrays, facility can print arrays of your material in high throughput fashion, including proteins, peptides, antibodies, cell lysates, siRNAs, etc.

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• SciCrunch
• 17 years ago - by Anonymous

ADFS is a web server system that integrates a database of allergenic proteins for food safety. This allergen database for food safety was launched as a project of the Novel Foods and Immunochemistry of National Institute of Health Sciences, and this project was partly supported by a grant from the Ministry of Health, Labor and Welfare. To survey the sequence homology in assessing a potential of allergenicity of a protein in the food, the database has been constructed to include known allergens and B-cell epitope sequences. This database includes 13 (aero animal, aero fungi, aero insect, aero mite, aero plant, contact, food animal, food fungi, food plant, gliadin, protozoan, venom/salivary, and worm) categorized allergens based on allergen type in AllergenOnline, with their accession numbers, epitope information, 3D-structure information, and sugar-containing information . This site also provides sequence search tools for obtaining the sequence homology of a certain protein or peptide relating to allergens (BLAST, epitope(peptide) search). Furthermore, this site provides allergenicity prediction tools of a certain protein (FAO/WHO method, Motif-based method).

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• SciCrunch
• 17 years ago - by Anonymous

A commercial distributed memory object caching system, generic in nature, but originally intended for use in speeding up dynamic web applications by alleviating database load. memcached allows you to take memory from parts of your system where you have more than you need and make it accessible to areas where you have less than you need. With memcached, you can see that all of the servers are looking into the same virtual pool of memory. This means that a given item is always stored and always retrieved from the same location in your entire web cluster.

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• SciCrunch
• 17 years ago - by Anonymous

Python 2D plotting library which produces publication quality figures in variety of hardcopy formats and interactive environments across platforms. Used in python scripts, web application servers, and six graphical user interface toolkits. Used to generate plots, histograms, power spectra, bar charts, error charts, scatter plots.

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• SciCrunch
• 13 years ago - by Anonymous

Software application (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

In many respects, this book will be an extension of many of the preoccupations Ive pursued here at Epidemix. Those handful of you who follow my magazine writing will no doubt recognize the theme as well. The premise is that we are at a new phase of health and medical care, where more decisions are being made by individuals on their own behalf, rather than by physicians, and that, furthermore, these decisions are being informed by new tools based on statistics, data, and predictions. This is a good thing it will let us, the general public, live better, happier, and even longer lives. But it will require us to be stewards of our health in ways we may not be prepared for. We will act on the basis of risk factors and predictive scores, rather than on conventional wisdom and doctors recommendations. We will act in collaboration with others, drawing on collective experience with health and disease, rather than in the isolation and ignorance that can come with privacy concerns. And we will act early, well before symptoms appear, opting to tap the science of genomics and proteomics in order to mitigate our risks down the road. Together, these tools will create a new opportunity and a new responsibility for people to act to make health decisions well before they become patients. This can be characterized as a decision tree, a series of informed choices we will make to minimize uncertainty and optimize our outcomes. Indeed, we will use decision trees to navigate most of our health decisions, sometimes in overt ways new decision support tools will both inform us and guide us, and theyll be steeped in statistics, predicition, and the power of collective experience.

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• SciCrunch
• 17 years ago - by Anonymous

SNPSpD is a method of correcting for non-independance of single nucleotide polymorphisms (SNPs) in linkage disequilibrium (LD) with each other, on the basis of the spectral decomposition (SpD) of matrices of LD between SNP''s. Additionally, output from SNPSpD includes eigenvalues, principal-component coefficients, and factor loadings after varimax rotation, enabling the selection of a subset of SNPs that optimize the information in a genomic region.

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• SciCrunch
• 16 years ago - by Anonymous

This portal runs on a processor cluster and allows Biochemists to use our parallel implementation of Clustal W together with our parallel implementation of Minimum Vertex Cover.

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• SciCrunch
• 17 years ago - by Anonymous

Gnuplot is a portable command-line driven graphing utility for linux, OS/2, MS Windows, OSX, VMS, and many other platforms. The source code is copyrighted but freely distributed (i.e., you don''t have to pay for it). It was originally created to allow scientists and students to visualize mathematical functions and data interactively, but has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like Octave. Gnuplot has been supported and under active development since 1986. Gnuplot supports many types of plots in either 2D and 3D. It can draw using lines, points, boxes, contours, vector fields, surfaces, and various associated text. It also supports various specialized plot types. Demos here. Gnuplot supports many different types of output: interactive screen terminals (with mouse and hotkey input), direct output to pen plotters or modern printers, and output to many file formats (eps, fig, jpeg, LaTeX, metafont, pbm, pdf, png, postscript, svg, ...). Gnuplot is easily extensible to include new output modes. Recent additions include an interactive terminal based on wxWidgets and the creation of mousable graphs for web display using the HTML5 canvas element.

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• SciCrunch
• 17 years ago - by Anonymous

The DNA Alignment software and Network software is used by biologists, anthropologists, medical researchers and students world wide. We carry out phylogeographic consultancy for US, UK and German clients, including legal medical work. We were involved in the tv projects The Real Eve (Discovery Channel) and Motherland (BBC). Our biotechnological director Dr Peter Forster is on the editorial board of the International Journal of Legal Medicine since 1999.

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• SciCrunch
• 17 years ago - by Anonymous

Provides summary of gene and genomic information from eukaryotic organism databases. This includes gene symbol and full name, chromosome, genetic and molecular map information, Gene Ontology (Function/Location/Process) and gene homology, product information, links to extended gene information.

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• SciCrunch
• 17 years ago - by Anonymous

emPAI (exponentially modified protein abundance index), developed by Ishihama et al., is a measure to describe the protein composition in sample solutions. When the total protein amount in the sample is available, emPAI can be converted to the absolute amount of each protein in the sample. emPAI is derived from PAI, which is defined as the number of the observed peptides divided by the number of the observable peptides per protein. We recently found that log (PAI) had linear relationship to the protein amounts, and that emPAI, 10^(PAI)-1, was proportional to the protein amounts for whole cell lysate digested by trypsin. The accuracy of this method was within factor 5, similar or better than determination of abundance by protein staining

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A database which contains the information of heparin-binding proteins of E. coli K-12 MG1655 cells. Heparin affinity columns were applied to enrich and fractionate proteins. Identification of proteins was done via the collaboration with David Russell''s lab. Because heparin is negatively charged sulfated glucosaminoglycan, polyamion binding proteins, which contain nucleic acid-binding proteins, are expected to bind to heparin columns. Study of the expression pattern of heparin-binding proteins will help to study the nucleic acid-binding proteins, most of which are related to regulation. Moreover, heparin affinity columns will also erich low abundance proteins. Heparome database is constructed using MySQL. Website interface is built using HTML and PHP. Queries between MySQL database and website interface are executed using PHP. Besides including information of identified proteins, such as swiss accession number, gene name, molecular weight, isoelectric point, condon adaptation index (CAI), functional classification, et. al. , it also includes information of experiments, such as sample preparation, heparin-HPLC chromatography, SDS-PAGE gel separation and MALDI-MS.

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• SciCrunch
• 17 years ago - by Anonymous

DISABKIDS is a European project which aims at enhancing the quality of life and the independence of children with chronic health conditions and their families. The project proceeds according to three phases: 1. Development of an instrument (paper/pencil as well as a computer assisted version) to assess quality of life and patient needs in children/adolescents with chronic health conditions. 2. Psychometric testing of the developed instrument in the 7 pariticipating countries in a pilot study with 378 children/ adolescents and a subsequent field study with 1260 children/adolescents and their families (180 families in each country). 3. Implementation and Evaluation of the instrument in routine care The project expects to achieve progress in quality of life assessment in children and adolescents with disabilities a) by focussing on an European co-operation in construction of an assessment instrument for quality of life, in which the persons concerned (children/adolescents and their families) play a major role, b) by addressing needs for care as explicitly voiced by the persons concerned, c) by including psychosocial as well as clinical and socio-economic determinants of quality of life and d) by developing a mode of administration which is practicable for the patient group concerned, so that in using the instrument, current care can be evaluated and future care can be improved by corresponding to the patients'' needs. Sponsors: The DISABKIDS project funded by the European Commission within the Fifth Framework Programme (FP5)

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• SciCrunch
• 17 years ago - by Anonymous

Sponsor:<BR/> support is NIH grant R01 GM077122<BR/> National Institutes of Health, Claudia Adams Barr Program, and Friends of DFCI.<BR/> We are interested in how genomics changes promote cancer progression. Through collaboration with biomedical researchers, we analyze high-throughput microarray and sequencing data to study genomics, expression, and network changes in cancer cells. New methods are packaged into widely-used software such as dChip, which has been cited more than 1600 times.<BR/>

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• SciCrunch
• 17 years ago - by Anonymous

A simple program for finding nearly matched primers Sponsor: This material is based upon work supported by the National Science Foundation under Grant No. 0114726.

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• SciCrunch
• 17 years ago - by Anonymous

It is a collaboration between owners, breeders and scientists with the goal of studying the genetics of the Portuguese Water Dog. The Georgie project sends out periodic reports of our findings. These reports are generally sent to the participants along with detailed information on their dogs. Here we have reproduce the public versions of the report for your reference.

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• SciCrunch
• 14 years ago - by Anonymous

A database and analysis of the brainwaves of individuals with pronounced physical disabilities. BrainGate''s mission is to further the advancement of this life-changing technology to promote wider adoption to help impaired individuals communicate and interact with society. For instance, the Cyberkenetics BrainGate Neural Interface is currently the subject of a pilot clinical trial being conducted under an Investigational Device Exemption (IDE) from the FDA. The system is designed to restore functionality for a limited, immobile group of severely motor-impaired individuals. It is expected that people using the BrainGate System will employ a personal computer as the gateway to a range of self-directed activities. These activities may extend beyond typical computer functions (e.g., communication) to include the control of objects in the environment such as a telephone, a television and lights. BrainGate offers a systems approach which applies the language of neurons in both short and long-term settings. The platform technology is based on the results of several years of research and development at premier academic institutions such as Brown University, the Massachusetts Institute of Technology, Emory University, and the University of Utah.

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• SciCrunch
• 17 years ago - by Anonymous

The CpG island searcher screens for CpG islands which meet the criteria selected below in submitted DNA sequences. Abstract The unique variability in the 5'' region of the GR gene, with 9 alternative first exons and 13 splice variants plays a critical role in transcriptional control maintaining homeostasis of the glucocorticoid receptor (GR). This 5''mRNA heterogeneity, common to all species investigated, remains untranslated since the alternative first exons are spliced to exon 2 immediately upstream of the translation initiation codon. These alternative first exons are located either immediately upstream of the coding exons in the CpG island (exons B-H and J), or further upstream (exons 1A and 1I). The mechanisms regulating the differential usage of these first exons in different tissues and individuals, and the role of the 5''UTR in the splicing of the coding exons are still poorly understood. Here we review some of the mechanisms that have so far been identified. Data from our laboratory and others have shown that the multiple first exons represent only a first layer of complexity orchestrated probably by tissue-specific transcription factors. Modulation of alternative first exon activity by epigenetic methylation of their promoters represents a second layer of complexity at least partially controlled by perinatal programming. The alternative promoter usage also appears to affect the 3'' splicing generating the different GR coding variants, GRalpha, GRbeta, and GR-P. Aberrant GR levels are associated with stress-related disorders such as depression, and affect social behaviour, mood, learning and memory. Dissecting how tissue-specific GR levels are regulated, in particular in the brain, is a first step to understand the significance of aberrant GR levels in disease and behaviour. Copyright 2010. Published by Elsevier Inc.

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• SciCrunch
• 17 years ago - by Anonymous