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A computational tool for calculating probability of variants in family-based sequencing data.

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• SciCrunch
• 13 years ago - by Anonymous

A software program to detect SNPs and short indels from pooled sequencing data generated using next-generation sequencing instruments.

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• SciCrunch
• 13 years ago - by Anonymous

A computational tool that analyzes the depth-of-coverage of high-throughput DNA sequencing reads, and can integrate paired-end and breakpoint junction analysis based CNV-analysis approaches, to infer locus copy-number genotypes.

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• SciCrunch
• 13 years ago - by Anonymous

A software package designed for the downstream analysis of short read mapping data produced by the ABI SOLiD and Illumina sequencing platforms.

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• SciCrunch
• 13 years ago - by Anonymous

A next-generation sequencing suite of variant analysis tools specializing in the separation of true SNPs and insertions and deletions (indels) from sequencing and mapping errors in WECS data.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package as de novo genomic assembler for short read sequencing technologies using de Bruijn graphs. Takes in short read sequences, removes errors, then produces high quality unique contigs, retrieves repeated areas between contigs. Can leverage very short reads in combination with read pairs to produce useful assemblies. Operating system Unix/Linux., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 13 years ago - by Anonymous

A new De Novo DNA sequence assembler based on global search-methods in order to contain the complexity of the assembly problem.

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• SciCrunch
• 13 years ago - by Anonymous

Software designed to help leverage the information from short sequences reads by stringently clustering them into contigs that can be used to characterize novel sequencing targets.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 24,2023. Software tool for de novo assembly of human genomes with massively parallel short read sequencing.Short-read assembly method that can build de novo draft assembly for human sized genomes.Software package for assembling short oligonucleotide into contigs and scaffolds., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 13 years ago - by Anonymous

A De Novo Next Generation Genomic Sequence Assembler Based on String Graph and MapReduce Cloud Computing Framework.

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• SciCrunch
• 13 years ago - by Anonymous

A de novo whole-genome shotgun (WGS) DNA sequence assembler.

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• SciCrunch
• 13 years ago - by Anonymous

Data analysis service for the standardized analysis of the immunoglobulin (IG) and T cell receptor (TR) rearranged nucleotide sequences. It identifies the variable (V), diversity (D) and joining (J) genes and alleles by alignment with the germline IG and TR gene and allele sequences of the IMGT reference directory. New functionalities were added through a complete rewrite in Java. IMGT/V-QUEST analyses batches of sequences (up to 50) in a single run. IMGT/V-QUEST describes the V-REGION mutations and identifies the hot spot positions in the closest germline V gene. IMGT/V-QUEST can detect insertions and deletions in the submitted sequences by reference to the IMGT unique numbering. IMGT/V-QUEST integrates IMGT/JunctionAnalysis for a detailed analysis of the V-J and V-D-J junctions, and IMGT/Automat for a full V-J- and V-D-J-REGION annotation. IMGT/V-QUEST displays, in ''Detailed view'', the results and alignments for each submitted sequence individually and, in ''Synthesis view'', the alignments of the sequences that, in a given run, express the same V gene and allele.

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• SciCrunch
• 13 years ago - by Anonymous

A biobank created from a cross-sectional population of a town in Sweden. The Medical Biobank is mainly based on three cohorts: The V��sterbotten intervention cohort, the MONICA-cohort, and the Mammary screening cohort. These sub-cohorts together are named Northern Sweden Health and Disease Study Cohort (North Health). These sub-cohorts together is named Northern Sweden Health and Disease Study Cohort (North Health). Originally, the V��sterbotten Intervention program (VIP) is a long-term project intended for health promotion of the population of V��sterbotten. All individuals 40, 50 and 60 years of age in the population of the county are invited for screening (approx. 254.000 inhabitants). They are asked to complete a questionnaire concerning various lifestyle factors including diet. They are also asked to donate a separate blood sample to the Medical Biobank for freeze storage for later research purposes. The project started in 1985 and the cohort covered in December 2002, 74,000 individuals, of whom 67,000 had donated blood samples. The material is supplemented with population based samples from a local mammary screening (44,000 sampling occasions, 25,700 unique individuals) and from the Northern Sweden MONICA Project (11,500 sampling occasions, 7,500 unique individuals). The total cohort contains at the moment 85.000 unique individuals with 130.000 sampling occasions. The VIP and MONICA cohorts are population based and the mammary screening cohort are nearly population based. Follow-up: * For the VIP-cohort a second sample (and questionnaire) is collected with a 10-year interval of the individuals within the cohort. * Repeated sampling was performed in the MONICA project in 1999 on individuals participating in 1986, 1990, and 1994. * From 1997 repeated screening has started within the mammary screening program with sampling every second year, in the age group 50-69 years within the county. Biobank content: * Life-Style Questionnaire: Every attending subject is asked to answer a questionnaire, which in the VIP and MONICA-projects includes questions about education, occupation/working conditions, daily habits including smoking, diet, etc and in the mammary screening cohort on reproductive conditions. The dietary questionnaire has been validated twice. The data from the questionnaires, as well as from results from the biobank, are kept in a database for future research purposes. The questionnaires in the VIP and the MONICA project are optically read. * Measurements: Blood Pressure, Anthropometry, Glucose Tolerance Test, Blood Lipids * Blood Samples: The attendants are asked for their willingness to donate a sample of 20-ml whole blood for future analyses. The sample is taken after 4 hours of fasting or in the morning after an over night fasting (most samples) in the VIP and MONICA cohorts. The 20-ml sample is divided into 10 subsamples consisting of 6 plasma, 2 leukocyte (buffy coat) and 2 erythrocyte samples. All material is frozen at -80 degrees C. The organization of the bank is elaborated with specially trained staff and an organization of transport-, storage- and security facilities. For DNA handling a specialized laboratory has been built up. * End-points: Mortality, Cancer events, Cardiovascular events, Other morbidity, Other registry-based follow-up * Registries: At regular intervals the cohort is scanned for incident myocardial infarctions (MI) and stroke utilizing the Northern Sweden MONICA registry and for cancer using the regional cancer registry. In the future the same procedure will be applied also on other registries e.g. diabetes, osteoporosis, dementia.

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• SciCrunch
• 16 years ago - by Anonymous

Biomaterial supply resource which provides high quality and well-chracaterized brain tissue samples for MS research. Registered MS brain donors and their families are kept up to date on the latest progress in MS research.

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• SciCrunch
• 16 years ago - by Anonymous

A provider of bio-implants and organs for transplantation and tissue banking services.

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• SciCrunch
• 16 years ago - by Anonymous

A core laboratory facility provides high-volume, high-quality tissue and biospecimen preparation and processing in support of Mayo research. Mayo Validation Support Services utilizes these resources to deliver extensive validation capabilities specific to individualized Sponsor requirements. Medical scientific expertise at Mayo Clinic allows for unique collaborations combining quality biospecimens linked to comprehensive clinical outcomes. Biospecimens can be accessed via archives or prospectively collected via individualized standard operating procedures. Patient information for all biospecimens is protected through oversight by an Institutional Review Board (IRB). Specimens may be collected and/or processed in a variety of customized formats for individual collaborations. Typical formats include: * Specimen Processing: Tissue RNA/DNA extraction capabilities, Paraffin and frozen sectioning, Immunostaining, Digital imaging, Laser capture microdissection, Tissue microarray construction, Preparation of protocol-collected tissue (FFPE, OCT, Snap-frozen, PBS) * Blood: Circulating tumor cells, Serum, Plasma, PBMC, Whole blood for FACS analysis, Blood smears * Other: Induced sputum, Saliva, Buccal swabs, Lip biopsies, Colonoscopy biopsies, Synovium, Stool, Urine Biospecimens located within archives are well-characterized and associated with phenotypic information. Multiple types and formats of biospecimens are available for customized validation purposes.

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• SciCrunch
• 16 years ago - by Anonymous

Not yet vetted by NIF curator

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• SciCrunch
• 16 years ago - by Anonymous

MEFIT is a Microarray Experiment Functional Integration Technology. Given any amount of microarray data, it predicts the probability of pairwise functional relationship for any gene pair within individual biological functions. This web site makes the results of this evaluation available for download and provides an online view of the test set predictions based on hierarchical clustering. As a framework, MEFIT uses the results of many microarray experiments in combination with known biological process annotations (drawn from the Gene Ontology, KEGG, MIPS, or a biologist''s own pathways of interest) to predict new gene pair functional relationships within the given biological functions. Or in other words, MEFIT is a system that takes microarray results and known functional annotations as inputs and produces predicted gene pair functional relationships as output. To make these predictions, MEFIT uses a Bayesian network that consumes microarray data as input observations and produces predicted functional relationships through a single unobserved (except during training) node. Furthermore, to make predictions within the context of individual biological functions, a single Bayesian network structure is replicated once per function of interest. These networks with identical structure are then trained using known functional annotations such that each function''s network learns its own set of conditional probabilities. These probabilities encode how predictive each microarray experiment is of a particular function; for example, a sporulation time course might be very predictive of meiosis, but not much help in determining which genes perform ATP synthesis. We''ve evaluated this system using a collection of 40 microarray data sets and 200 biological processes. Select a biological function from the menu to view the results of clustering the S. cerevisiae genome using MEFIT''s test set predictions within that function as a similarity metric. Alternatively, enter a gene name or ORF identifier to list only functions in which that gene is predicted to be active. We are currently able to offer for download: The MEFIT README file, a Windows version and Linux version.

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• SciCrunch
• 16 years ago - by Anonymous

Software tool as whole genome shotgun assembler that can generate high quality genome assemblies using short reads (~100bp) such as those produced by the new generation of sequencers.

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• SciCrunch
• 13 years ago - by Anonymous

Commercial tissue bank for human tissues.

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• SciCrunch
• 16 years ago - by Anonymous