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THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The aim of this locus-specific mutation database was to provide an online resource that contains summarized and updated information on familial hypertrophic cardiomyopathy (FHC)-associated mutations and related data, for researchers and clinicians. It also serves as a means of publishing previously unpublished data, which could be of value in understanding genotype/phenotype correlations. This database contains mutations in various genes known to cause familial hypertrophic cardiomyopathy, a genetic disorder associated with defects in the sarcomere [1]. Only gene symbols approved by HUGO are used and mutations are reported in accordance with guidelines recommended by the Mutation Database Initiative of HUGO and EBI.

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• SciCrunch
• 17 years ago - by Anonymous

Database of experimentally validated gene regulatory relations and the corresponding transcription factor binding sites upstream of Bacillus subtilis genes. The database allows the comparison of systematic experiments with individual experimental results in order to facilitate the elucidation of the complete B. subtilis gene regulatory network. The current version is constructed by surveying 947 references and contains the information of 120 binding factors and 1475 gene regulatory relations. For each promoter, all of its known cis-elements are listed according to their positions, while these cis-elements are aligned to illustrate the consensus sequence for each transcription factor. All probable transcription factors coded in the genome were classified using Pfam motifs. The DBTBS database was reorganized to show operons instead of individual genes as the building blocks of gene regulatory networks. It now contains 463 experimentally known operons, as well as their terminator sequences if identifiable. In addition, 517 transcriptional terminators were identified computationally. (De Hoon, M.J.L. et al., PLoS Comput. Biol. 1, e25 (2005)). A new section was added under "Motif conservation", which presents hexameric motifs found to be conserved to different extents between upstream intergenic regions of genus-specific subgroups of homologous proteins.

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• SciCrunch
• 13 years ago - by Anonymous

Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. ELISA is an online database that combines functional annotation with structure and sequence homology modeling to place proteins into sequence-structure-function neighborhoods. The atomic unit of the database is a set of sequences and structural templates that those sequences encode. A graph that is built from the structural comparison of these templates is called PDUG (protein domain universe graph). It introduces a method of functional inference through a probabilistic calculation done on an arbitrary set of PDUG nodes. Further, all PDUG structures are mapped onto all fully sequenced proteomes allowing an easy interface for evolutionary analysis and research into comparative proteomics. ELISA is the first database with applicability to evolutionary structural genomics explicitly in mind.

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• SciCrunch
• 17 years ago - by Anonymous

Whole Genome Simulator for Next-Generation Sequencing.

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• SciCrunch
• 13 years ago - by Anonymous

Software tool that not only compresses FASTQ-formatted DNA reads more compactly than gzip but also permits rapid search for k-mer queries within the archived sequences. The full FASTQ record of each matching read or read pair is returned, allowing the search results to be piped directly to any of the many standard tools that accept FASTQ data as input. Searchable compressed archive for DNA reads.

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• SciCrunch
• 12 years ago - by Anonymous

A program for registering images with with mutual information based metric. Several registration options are given for 3,6, 9,12,16 parameter (i.e. translate, rigid, scale, scale/skew, full affine) based constraints for the registration. The program uses the Slicer3 execution model framework to define the command line arguments and can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3

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• SciCrunch
• 13 years ago - by Anonymous

A database of protein subcellular localization containing proteins from primary protein database SWISS-PROT and PIR. By collecting the subcellular localization annotation, these information are classified and categorized by cross references to taxonomies and Gene Ontology database. Annotations were taken from primary protein databases, model organism genome projects and literature texts, and then were analyzed to dig out the subcellular localization features of the proteins. The proteins are also classified into different categories. Based on sequence alignment, nonredundant subsets of the database have been built, which may provide useful information for subcellular localization prediction. The database now contains >60 000 protein sequences including 30 000 protein sequences in the nonredundant data sets. Online download, SOAP server, Blast tools and prediction services are also available.

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• SciCrunch
• 17 years ago - by Anonymous

General database of genetic variations maintained by the NCBI. Database as central repository for both single base nucleotide substitutions and short deletion and insertion polymorphisms. Distinguishes report of how to assay SNP from use of that SNP with individuals and populations. This separation simplifies some issues of data representation. However, these initial reports describing how to assay SNP will often be accompanied by SNP experiments measuring allele occurrence in individuals and populations. Community can contribute to this resource.

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• SciCrunch
• 17 years ago - by Anonymous

Software program that compares fluorescence-based sequences across traces obtained from different individuals to identify heterozygous sites for single nucleotide substitutions. Its functions are integrated with the use of three other programs: Phred (Brent Ewing and Phil Green), Phrap (Phil Green), and Consed (David Gordon and Phil Green). PolyPhred identifies potential heterozygotes using the base calls and peak information provided by Phred and the sequence alignments provided by Phrap. Potential heterozygotes identified by PolyPhred are marked for rapid inspection using the Consed tool.

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• SciCrunch
• 13 years ago - by Anonymous

Table designed as a hypothesis testing, teaching and reference tool for physicians and researchers interested in drug interactions that are the result of competition for, or effects on the human cytochrome P450 system. The table contains lists of drugs in columns under the designation of specific cytochrome P450 isoforms. A drug appears in a column if there is published evidence that it is metabolized, at least in part, via that isoform. It does not necessarily follow that the isoform is the principal metabolic pathway in vivo, or that alterations in the rate of the metabolic reaction catalyzed by that isoform will have large effects on the pharmacokinetics of the drug., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 17 years ago - by Anonymous

Parasite-related portal including concise reviews of parasites and parasitic diseases, an image library, a review of recommended procedures for collecting, shipping, processing, and examining biologic specimens, and a diagnostic assistance function, in which laboratorians and other health professionals desiring assistance in parasite identification can ask questions and/or send digital images of specimens for expedited review and consultation with DPD staff. This assistance is free of charge. The portal is hoped to strengthen diagnosis of, and enhance the capacity to address the global problem of parasitic diseases, both in the United States and abroad. Potential DPDx applications include: * training and continuing education of laboratorians, using material collected by CDC or contributed by other institutions * provision to health facilities worldwide of diagnostic assistance by CDC staff backed up when needed by experts from other institutions * diagnostic quizzes for self-assessment of laboratorians skills * informal, early detection of unusually clustered, atypical or emerging parasitic diseases

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• SciCrunch
• 17 years ago - by Anonymous

DoTS (Database Of Transcribed Sequences) is a human and mouse transcript index created from all publicly available transcript sequences. The input sequences are clustered and assembled to form the DoTS Consensus Transcripts that comprise the index. These transcripts are assigned stable identifiers of the form DT.123456 (and are often referred to as dots). The transcripts are in turn clustered to form putative DoTS Genes. These are assigned stable identifiers of the form DG.1234356. As of September 1, 2004, the DoTS annotation team has manually annotated 43,164 human and 78,054 mouse DoTS Transcripts (DTs), corresponding to 3,939 human and 7,752 mouse DoTS Genes (DGs). Use the manually annotated gene query to see the DoTS Transcripts that have been manually annotated. The focus of the DoTS project is integrating the various types of data (e.g., EST sequences, genomic sequence, expression data, functional annotation) in a structured manner which facilitates sophisticated queries that are otherwise not easy to perform. DoTS is built on the GUS Platform which includes a relational database that uses controlled vocabularies and ontologies to ensure that biologically meaningful queries can be posed in a uniform fashion. An easy way to start using the site is to search for DoTS Transcripts using an existing cDNA or mRNA sequence. Click on the BLAST tab at the top of the page and enter your sequence in the form provided. All the transcripts with significant sequence similarity to your query sequence will be displayed. Or use one of the provided queries to retrieve transcripts using a number of criteria. These queries are listed on the query page, which can also be reached by clicking on the tab marked query at the top of the page. Finally, the boolean query page allows these queries to be combined in a variety of ways. Sponsors: Funding provided by -NIH grant RO1-HG-01539-03 -DOE grant DE-FG02-00ER62893

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• SciCrunch
• 17 years ago - by Anonymous

Software using a de novo repeat assembly method which avoids potential biases by using abundant k-mers of next-generation sequencing (NGS) whole genome sequencing (WGS) reads without requiring a reference genome.

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• SciCrunch
• 12 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. An international collaboration between 46 labs from 20 different countries towards a low resolution canine marker map under the auspices of the International Society for Animal Genetics (ISAG). The map under development should achieve a resolution of about 20 cM and some of the markers should be mapped physically. The participants have agreed to use microsatellites as markers on a common panel of reference families which will provide the backbone of the marker map. It is foreseen to also include type I markers in the mapping effort and to produce cosmid derived microsatellites for physical mapping. For this purpose part of the effort focuses on the standardization of the canine karyotype. Special attention is payed to hereditary diseases where efforts are under way to establish resource families either by collecting families or by specific breeding. A point of emphasis of the DogMap project is the setting up of an internationally accessible database for handling the mapping data. The structure of the DogMap collaboration includes a managing committee and scientific advisers. The managing committee is responsible for the overall coordination of the activities within the collaboration, for the dissemination of relevant information to all of the participants and for the representation of DogMap outside the collaboration., 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 July 15, 2016. Database containing location and descriptive information about a wide variety of information resources including organizations, research resources, projects, and databases concerned with health and biomedicine. This information may not be readily available in bibliographic databases. Each record may contain information on the publications, holdings, and services provided. These information resources fall into many categories including federal, state, and local government agencies; information and referral centers; professional societies; self-help groups and voluntary associations; academic and research institutions and their programs; information systems and research facilities. Topics include HIV/AIDS, maternal and child health, most diseases and conditions including genetic and other rare diseases, health services research and technology assessment. DIRLINE can be searched using subject words (such as disease or condition) including Medical Subject Headings (MeSH) or for the name or location of a resource. It now offers an A to Z list of over 8,500 organizations.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented June 26, 2017. Lab that provides resources for researchers such as image analysis and access to confocal microscopes.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 28, 2017.<br/><br/>Software that performs comparative sequencing, also known as direct sequencing, medical sequencing, PCR sequencing and resequencing with DNA sequencing files. The software is designed for reference based and non-reference based analysis such as mutation detection and analysis, SNP discovery and validation and sequence confirmation.

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• SciCrunch
• 13 years ago - by Anonymous

Commercial supplier of antibodies, assay kits, conjugates and various toxins for biomedical research. ATS's product line is designed to assist scientists in the study of system functions, cell functionality, diseases and disorders.

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• SciCrunch
• 14 years ago - by Anonymous

A biclustering algorithm that finds modules in an input matrix. A module or bicluster is a block of the reordered input matrix.

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• SciCrunch
• 12 years ago - by Anonymous