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A software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data.

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• SciCrunch
• 13 years ago - by Anonymous

A plant small RNA target analysis server which features two important analysis functions: 1) reverse complementary matching between miRNA and target transcript using a proven scoring schema, and 2) target site accessibility evaluation by calculating unpaired energy (UPE) required to ?open? secondary structure around miRNA?s target site on mRNA. PsRNATarget incorporates recent discoveries in plant miRNA target recognition, e.g. it distinguishes translational and post-transcriptional inhibition, and it reports the number of miRNA/target site pairs that may affect miRNA binding activity to target transcript. PsRNATarget is designed for high-throughput analysis of next-generation data with an efficient distributed computing back-end pipeline that runs on a Linux cluster. The server front-end integrates three simplified user-friendly interfaces to accept user-submitted or preloaded miRNAs and transcript sequences; and outputs a comprehensive list of miRNA / target pairs along with the online tools for batch downloading, key word searching and results sorting., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 13 years ago - by Anonymous

Data set of extensive information on the changing circumstances of aged and disabled beneficiaries - Living, noninstitutionalized population of the continental United States from the Social Security Administration''''s Master Benefit Record who were new recipients of Social Security benefits (first payment in mid-1980 through mid-1981) or who had established entitlement to Medicare and were eligible for, but had not received, Social Security benefits as of July 1982. Based initially on a national cross-sectional survey of new beneficiaries in 1982, the original data base was expanded with information from administrative records and a second round of interviews in 1991. Variables measured in the original New Beneficiary Survey (NBS) include demographic characteristics; employment, marital, and childbearing histories; household composition; health; income and assets; program knowledge; and information about the spouses of married respondents. The 1991 New Beneficiary Follow-up (NBF) updated marital status, household composition, and the economic profile and contains additional sections on family contacts, postretirement employment, effects of widowhood and divorce, major reasons for changes in economic status, a more extensive section on health, and information on household moves and reasons for moving. Disabled-worker beneficiaries were also asked about their efforts to return to work, experiences with rehabilitation services, and knowledge of SSA work incentive provisions. The NBDS also links to administrative files of yearly covered earnings from 1951 to 1992, Medicare expenditures from 1984 to 1999, whether an SSI application has ever been made and payment status at five points in time, and dates of death as of spring 2001. For studies of health, the Medicare expenditure variables include inpatient hospital costs, outpatient hospital costs, home health care costs, and physicians'''' charges. The survey data cover functional capacity including ADLs and IADLs. For studies of work in retirement, the survey includes yearly information on extent of work, characteristics of the current or last job, and reasons for working or not working. No other data set has such detailed baseline survey data of a population immediately after retirement or disability, enhanced with subsequent measures over an extended period of time. The data are publicly available through NACDA and the Social Security Administration Website. * Dates of Study: 1982-1991 * Study Features: Longitudinal * Sample Size: ** 18,136 (NBS 1981) ** 12,677 (NBF 1991) Links: * 1982 (ICPSR): http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/08510 * 1991 (ICPSR): http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06118

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• SciCrunch
• 14 years ago - by Anonymous

An Antibody supplier

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• SciCrunch
• 14 years ago - by Anonymous

An Antibody supplier and subset of ThermoFisher Scientific which provides fluorescence reagents for various experiments and methods.

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• SciCrunch
• 14 years ago - by Anonymous

Center to advance research and training in mathematical, computational and modern imaging approaches to understanding the brain and its functions. Software tools and associated reconstruction data produced in the center are available. Researchers study the relationships between neural function and structure at levels ranging from the molecular and cellular, through network organization of the brain. This involves the development of new computational and analytic tools for imaging and visualization of 3-D neural morphology, from the gross topologic characteristics of the dendritic arbor to the fine structure of spines and their synapses. Numerical simulations of neural mechanisms based on these structural data are compared with in-vivo and in-vitro electrophysiological recordings. The group also develops new theoretical and analytic approaches to exploring the function of neural models of working memory. The goal of this analytic work is to combine biophysically realistic models and simulations with reduced mathematical models that capture essential dynamical behaviors while reproducing the functionally important features of experimental data. Research areas include: Imaging Studies, Volume Integration, Visualization Techniques, Medial Axis Extraction, Spine Detection and Classification, Applications of Rayburst, Analysis of Spatially Complex Structures, Computational Modeling, Mathematical and Analytic Studies

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• SciCrunch
• 17 years ago - by Anonymous

A software tool optimized for mapping short RNAs onto a reference genome.

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• SciCrunch
• 13 years ago - by Anonymous

An accurate and efficient algorithm for discovering canonical and non-canonical splice junctions in short read datasets.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. FusionDB is a database of bacterial and archaeal gene fusion events - also known as Rosetta stones. Gene-fusion events are not the only resource to determine functional links between two proteins. Similar phylogenetic profiles and conserved chromosomal co-localization can also be used as an indicator for such interactions.

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• SciCrunch
• 17 years ago - by Anonymous

Francisella tularensis is a Gram-negative bacteria that causes the disease tularemia. The genus also includes the strains Francisella novicida and Francisella holarctica, both of which are important research organisms. The biology, genomes and virulence capabilities of these organism are under active investigation in research institutions throughout the world. Our goal for the francisella.org website is to foster communication and collaboration among the Francisella tularensis research community. rancisella tularensis is a Gram-negative bacteria that causes the disease tularemia. The genus also includes the strains Francisella novicida and Francisella holarctica, both of which are important research organisms. The biology, genomes and virulence capabilities of these organism are under active investigation in research institutions throughout the world. Our goal for the francisella.org website is to foster communication and collaboration among the Francisella tularensis research community. Please visit the following sections of the website for more details about the tools currently available and those to be available in the near future. News 04/17/2008 F. novicida transposon mutant orders are now being handled by BEI Resources. 03/25/2008 New features have been added to the PSAT synteny analysis tool including a printer friendly version of the genomic neighborhood graphic, a text output of homologs in a region in spreadsheet format, and an option for displaying multiple alignments for a gene against a single comparison genome. 02/07/2008 Proteomics experimental data for F. novicida are now integrated into our genome browser. 02/05/2008 Updated genome annotations can now be submitted using the Panda tool. Your participation is encouraged. Please see the Panda page for more information. 02/04/2008 F. holarctica FTA is now available from Genbank (NC_009749) and has been added to our genome browser Tools Name Description Get surrounding sequence Given a gene, other genome feature, or genome coordinate, displays in FASTA format the surrounding sequence a specified number of nucleotides upstream and downstream Synteny Tool Analyze potential regions of local synteny between the Francisella genomes and any other published bacterial genome

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• SciCrunch
• 17 years ago - by Anonymous

An authoritative and comprehensive list of names of marine organisms, including information on synonymy. While highest priority goes to valid names, other names in use are included so that this register can serve as a guide to interpret taxonomic literature. The content of WoRMS is controlled by taxonomic experts, not by database managers. WoRMS has an editorial management system where each taxonomic group is represented by an expert who has the authority over the content, and is responsible for controlling the quality of the information. Each of these main taxonomic editors can invite several specialists of smaller groups within their area of responsibility to join them. This register of marine species grew out of the European Register of Marine Species (ERMS), and its combination with several other species registers maintained at the Flanders Marine Institute (VLIZ). Rather than building separate registers for all projects, and to make sure taxonomy used in these different projects is consistent, VLIZ developed a consolidated database called ''Aphia''. A list of marine species registers included in Aphia is available below. MarineSpecies.org is the web interface for this database. The WoRMS is an idea that is being developed, and will combine information from Aphia with other authoritative marine species lists which are maintained by others (e.g. AlgaeBase, FishBase, Hexacorallia, NeMys). Resources to build MarineSpecies.org and Aphia were provided mainly by the EU Network of Excellence ''Marine Biodiversity and Ecosystem Functioning'' (MarBEF), and also by the EU funded Species 2000 Europe and ERMS projects. Intellectual property rights of the European part of the register is managed through the Society for the Management of Electronic Biodiversity Data (SMEBD). Similar solutions are now being investigated for the other parts of the register.

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• SciCrunch
• 13 years ago - by Anonymous

An Antibody supplier

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented September 15, 2017.\\\\\\<br/>\\\\\\<br/>An Antibody supplier.

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• SciCrunch
• 14 years ago - by Anonymous

Software application that is an interactive graphic interface to visualise results from whole genome genotyping. It allows one to visualise single subjects and groups of subjects, and provides a direct connection with the UCSC Genome Browser. (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

An Antibody supplier

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• SciCrunch
• 14 years ago - by Anonymous

A scalable software pipeline for whole genome resequencing analysis.

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• SciCrunch
• 13 years ago - by Anonymous

A specialized database for human alternative splicing (AS) based on H-Invitational full-length cDNAs. H-DBAS offers unique data and viewer for human Alternative Splicing (AS) analysis. It contains: * Genome-wide representative alternative splicing variants (RASVs) identified from following datasets * H-Inv full-length cDNAs (resource summary): H-Invitational cDNA dataset * H-Inv all transcripts (resource summary): Published human mRNA dataset * Mouse full-length cDNAs (resource summary): Mouse cDNA dataset * RASVs affecting protein functions such as protein motif, GO, subcellular localization signal and transmembrane domain * Conserved RASVs compared with mouse genome and the full-length cDNAs (H-Inv full-length cDNAs only)

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• SciCrunch
• 17 years ago - by Anonymous

Software application for performing genome scan meta-analysis, a quantitative method to identify genetic regions (bins) with consistently increased linkage score across multiple genome scans, and for testing the heterogeneity of the results of each bin across scans. The program provides as an output the average of ranks and three heterogeneity statistics, as well as corresponding significance levels. (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

Software application that implements a novel variable selection method for GWAS data and is able to handle more than half million SNPs. Extensive simulation studies and real data analysis show that this method enjoys high power and low false discovery rate compared to existing variable selection methods. The variables selected by GWASelect can be readily placed into a logistic regression model for disease prediction. The current release is designed for binary outcome under the additive mode of inheritance. (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

Medical school of the University of Pennsylvania. It is located in the University City section of Philadelphia.

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• SciCrunch
• 16 years ago - submitted by Andrea Stagg