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A gold-standard dataset of biologically relevant binding sites in protein structures. It consists of proteins with one unbound structure and at least one structure of the protein-ligand complex. Both a redundant and a non-redundant (sequence identity lower than 25) version is available. Quaternary structures proposed by PQS (2) are used for all structures in the dataset. The availability of both unbound and bound structures for each protein guarantees that our dataset can be used to benchmark binding site prediction methods, in conditions that mimic cases where the binding site is truly unknown. In cases where several different bound structures are available for a given protein, all are used to define the binding sites.

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• SciCrunch
• 17 years ago - by Anonymous

Fast and lightweight package for mapping bisulfite converted DNA sequencing reads from the Illumina platform.

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• SciCrunch
• 13 years ago - by Anonymous

A nucleotide sequence similiary search tool which is far faster than BLAST for large datasets, with only a marginal loss in search sensitivity.

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• SciCrunch
• 13 years ago - by Anonymous

A Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface (GUI).

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• SciCrunch
• 13 years ago - by Anonymous

We provide plasmid cloning services. Our procedures allow cloning not only by using restriction enzymes but also in restriction-enzymes-independent ways. This allows sequence modification in areas where no suitable restriction sites are present. Examples for services offered: - Amplification of insert from one plasmid and cloning in another plasmid. - Addition of sequence to an existing plasmid, for example adding FLAG+myc tags, restriction sites, linkers, shRNA coding sequences, can add up to 100 bp in one cloning operation. - Introducing site directed mutations, can modify multiple bases within a 50 bp sequence in one cloning operation. - Deletion of sequences of any length from a plasmid. - Insertion of one gene fragment in to another gene, for example for making a chimeric protein. - Cloning an insert in to a plasmid while adding a tag at the 5'' or 3'' ends of the insert. - Cloning an insert while adding a polyglycine spacer to prevent structural effects of tags on your protein. - Any other sequence modifications by request.

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• SciCrunch
• 13 years ago - by Anonymous

The Research Computing System is a vision for a user controlled collection of applications, tools, and services integrated through a uniform understanding of user identity and the communities (groups) to which the user belongs. This environment enables seamless access to shared resources and facilitates collaborations within departments, across campus and around the globe. The RCS development project is a collaborative effort to build a private cloud to support the construction and operation of research applications. RCS is the collection of these resources and the communities surrounding their development. RCS is an open development effort that welcomes participation of those interested in the construction, use, or operation of this platform.

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• SciCrunch
• 17 years ago - by Anonymous

Software tools and databases for plant genomics.

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• SciCrunch
• 13 years ago - by Anonymous

The National Center for Medical Rehabilitation Research (NCMRR) established a multi-center network of sites that are working together to design clinical intervention protocols and measures of outcome for TBI. Through rigorous patient evaluation, using common protocols and interventions designed for multiple points of care����??including the accident scene, emergency room, intensive care unit, rehabilitation and long-term follow-up����??the NCMRR TBI Clinical Trials Network can study the required numbers of patients to provide answers more rapidly than individual centers acting alone. This interdisciplinary research Network is designed to evaluate the relationship among acute care practice, rehabilitation strategies, and the long-term functional outcome of TBI patients����??that is, to identify which intervention variables result in improvements in long-term outcomes. Taking advantage of the network model structure has allowed TBI research to progress toward a number of clinical research goals. Specifically, the NCMRR wants to highlight two major achievements to date. First, the TBI Network created a profile of its typical patient to determine the number of patients with different clinical features who might be eligible for future studies and to help estimate recruitment times necessary. Second, Network researchers are developing clinical treatment guidelines and procedures for all points in the continuum of care, including TBI Clinical Trials Network Guidelines for surgical care, systems-based protocol for severe and moderate TBI patients, deep-vein thrombosis prophylaxis procedures, and rehabilitation guidelines for physical therapy, speech-language pathology, occupational therapy, and neuropsychology.

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• SciCrunch
• 15 years ago - by Anonymous

The HTPSELEX database contains sets of in vitro selected transcription factor binding site sequences obtained via a high-throughput SELEX (HTPSELEX) method. In addition, the database also contains binding sites obtained with conventional SELEX method. The database hosts 12 individual Selex libraries for the transcription factors CTF/NF1 and LEF/TCF families totaling more than 40,000 sites. In addition we also have manually curated SELEX datasets from the literature for 25 different transcription factors.

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• SciCrunch
• 17 years ago - by Anonymous

Cancer and many other human diseases arise from gene defects, which are either inherited or occur - as in most cancers spontaneously in somatic cells. These defects cause aberrant activities of gene products and malfunctioning of molecular and cellular interactions, thereby inducing tumors and accompanying cancer progression. The central objective of our division is to understand the complex molecular processes of human health and disease. In particular, we are working on tools for improving diagnosis of malfunctioning and prognosis for patients as well as the identification and validation of novel targets for therapies. Main interest of the division is on cellular signaling networks and their roles in cancer drug resistance and metastasis. To this end, we apply high-throughput functional genomics and proteomics technologies, and analyze candidate genes using in vitro and in vivo systems. The division organizes the conference Systems Genomics 2010 (September 29 - October 1, 2010 at the DKFZ Heidelbeg) and aims at advancing the integration of high-throughput genomics, quantitative proteomics, computational biology, and clinics. Internationally outstanding speakers will discuss their latest results in molecular and translational disease research Sponsor. This work was supported in part by the National Genome Research Network (Contract No. 01GS0864) of the Federal Ministry of Education and Research (BMBF) and by Wilhelm-Sander Stiftung (Contract No. 2009.051.1). JDZ is supported by the DKFZ International PhD Program. We thank Moritz Kblbeck, Christian Schmidt and Ute Ernst for their excellent technical assistance.

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• SciCrunch
• 17 years ago - by Anonymous

It is an international research infrastructure for investigators interested in conducting population and clinic-based interdisciplinary studies on the genetic and molecular epidemiology of colon cancer and its behavioral implications. A central goal of the C-CFR is the translation of this research to the clinical and prevention setting for the benefit of Registry participants and the general public. The C-CFR has information and biospecimens contributed by greater than 11,300 families across the spectrum of risk for colon cancers and from population-based or relative controls. Of particular interest are: identification and characterization of cancer susceptibility genes definition of gene-gene and gene-environment interactions in cancer etiology translational, preventive, and behavioral implications of research findings Special features include: population-based and clinic-based ascertainment systematic collection of validated family history epidemiologic risk factor data clinical and follow-up data biospecimens (including tumor blocks and EBV transformed cell lines) ongoing molecular characterization of the participating families Goals: to contribute to the development of public health measures for the general population by increasing knowledge on genetic factors affecting cancer susceptibility and modification by environmental and lifestyle factors to protect those with increased susceptibility from developing cancer to provide life-prolonging treatment to genetically susceptible individuals Objectives: to establish a comprehensive research resource infrastructure to assist with the implementation of collaborative, interdisciplinary research protocols in the genetic epidemiology of cancer to identify, characterize, and follow-up a cohort of individuals and their family members, spanning the spectrum of cancer risk to identify diverse genetically susceptible populations that could benefit from enrollment in preventive and therapeutic interventions to develop an adaptive and evolving informatics model to support ongoing and future research consortia Sponsor. This study was supported by National Cancer Institute Grants R01 CA47147, R01 CA47305, and R01 CA69664.

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• SciCrunch
• 14 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 32,2023.

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• SciCrunch
• 16 years ago - by Anonymous

A set of Java-based command-line tools for detecting Copy Number Variants (CNVs) using next-generation sequencing data.

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• SciCrunch
• 13 years ago - by Anonymous

BRAT is an accurate and efficient tool for mapping short bisulfite-treated reads obtained from the Solexa-Illumina Genome Analyzer.

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• SciCrunch
• 13 years ago - by Anonymous

To explore the elephant shark genome, we have conducted a survey-sequencing and comparative analysis of the elephant shark genome in collaboration with J. Craig Venter Institute. The elephant shark sequences generated under this project have been deposited at GenBank under the project accession number AAVX01000000. The sequences can also be searched using BLAST and retrieved here. Cartilaginous fishes (Chondrichthyes) represented by sharks, rays, skates and chimaeras, are phylogenetically the oldest group of living jawed vertebrates. They constitute an important group for our understanding of the origins of the complex developmental and physiological systems of jawed vertebrates. They are also an useful outgroup for bony vertebrates such as tetrapods and teleost fishes and help in identifying specialized features that have led to the evolution of diverse groups of bony vertebrates. The elephant shark (Callorhinchus milii), also known as the elephant fish and ghost shark, is a chimaera belonging to the Order Chimaeriformes and Family Callorhynchidae. It has the smallest genome among the known cartilaginous fish genomes. Thus, it was proposed as a model cartilaginous fish genome for whole-genome sequencing and comparative analysis (Venkatesh et al. 2005. Curr. Biol. 15: R82-R83). The following resources of the elephant shark are available for the scientific community: *Elephant Shark 1.4x assembly fasta sequences zipped 227 megabytes *Genomic DNA *~8x coverage BAC library (average insert size, ~150 kb) *cDNA libraries (under construction) *cDNA (dated 11 April 2008) with orthologs in 5 vertebrates (human, opossum, chicken, frog, fugu)

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• SciCrunch
• 17 years ago - by Anonymous

Database of zebrafish genome.

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• SciCrunch
• 16 years ago - by Anonymous

StemCore Laboratories is a high-throughput genomics facility within the Ottawa Hospital Research Institute (OHRI). StemCore Laboratories is developing a world-class infrastructure for genomics, bioinformatics, and proteomics, and is capable of facilitating large-scale scientific research and biotechnology projects. Stemcore Laboratories seeks out projects that are challenging, cutting-edge, extend the boundaries of biological knowledge, and will positively impact the state of human health. Funded: Genome Canada, The Ontario Genomics Institute, The Canadian Foundation for Innovation, The Government of Ontario, The Stem Cell Network, Stantive Solutions

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. Listing of computer software for the gene mapping community on the following topics: genetic linkage analysis for human pedigree data, QTL analysis for animal/plant breeding data, genetic marker ordering, genetic association analysis, haplotype construction, pedigree drawing, and population genetics. The inclusion of a program should not be interpreted as an endorsement to that program from us. In the last few years, new technology produces new types of genetic data, and the scope of genetic analyses change dramatically. It is no longer obvious whether a program should be included or excluded from this list. Topics such as next-generation-sequencing (NGS), gene expression, genomics annotation, etc. can all be relevant to a genetic study, yet be specialized topics by themselves. Though programs on variance calling from NSG can be in, those can sequence alignment might be out; programs on eQTL can be in, those on differential expression might be out. This page was created by Dr. Wentian Li, when he was at Columbia University (1995-1996). It was later moved to Rockefeller University (1996-2002), and now takes its new home at North Shore LIJ Research Institute (2002-now). The present copy is maintained by Jurg Ott as a single file. More than 240 programs have been listed by December 2004, more than 350 programs by August 2005, close to 400 programs by December 2006, and close to 480 programs by November 2008, and over 600 programs by October 2012. A version of the searchable database was developed by Zhiliang Hu of Iowa State University, and a recent round of updating was assisted by Wei JIANG of Harbin Medical School. Some earlier software can be downloaded from EBI: ftp://ftp.ebi.ac.uk/pub/software/linkage_and_mapping/ (Linkage and Mapping Software Repository), and http://genamics.com/software/index.htm may contain archived copy of some programs.

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• SciCrunch
• 17 years ago - by Anonymous

The Ensembl Genomes project produces genome databases for important species from across the taxonomic range, using the Ensembl software system. Five sites are now available, one of which is Ensembl Protists, which houses protists species. Sponsors: EnsembProtists is a project run by EMBL - EBI to maintain annotation on selected genomes, based on the software developed in the Ensembl project developed jointly by the EBI and the Wellcome Trust Sanger Institute.

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• SciCrunch
• 17 years ago - by Anonymous

Web application to discover resources available at participating networked universities. This distributed platform for creating and sharing semantically rich data is built around semantic web technologies and follows linked open data principles.

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• SciCrunch
• 16 years ago - by Anonymous