Curator Dashboard

The Node: a community site for development biologists

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• SciCrunch
• 16 years ago - by Anonymous

PhosphoNET is an open-access, online knowledgebase developed by Kinexus Bioinformatics Corporation to foster the study of cell signaling systems to advance biomedical research in academia and industry. PhosphoNET is the world''s largest repository of known and predicted information on human phosphorylation sites, their evolutionary conservation and the identities of protein kinases that may target these sites. Search by protein name, UniProt number, IPI number, or 15 AA P-site sequence. PhosphoNET presently holds data on over 650,000 known and putative phosphorylation sites (P-sites) in over 23,000 human proteins that have been collected from the scientific literature and other reputable websites. Over 14% of these phospho-sites have been experimentally validated. The rest have been predicted with a novel P-Site Predictor algorithm developed at Kinexus with academic partners at the University of British Columbia and Simon Fraser University. With the PhosphoNET Evolution module, this website also provides information about cognate proteins in over 20 other species that may share these human phospho-sites. This helps to define the most functionally important phospho-sites as these are expected to be highly conserved in nature. With the Kinase Predictor module, listings are provided for the top 50 human protein kinases that are likely to phosphorylate each of these phospho-sites using another proprietary kinase substrate prediction algorithm developed at Kinexus. Our kinase substrate predictions are based on deduced consensus phosphorylation site amino acid frequency scoring matrices that we have determined for each of ~500 different human protein kinases. The specificity matrices are generated directly from the primary amino acid sequences of the catalytic domains of these kinases, and when available, have proven to correlate strongly with substrate prediction matrices based on alignment of known substrates of these kinases. The higher the score, the better the prospect that a kinase will phosphorylate a given site. Over 30 million kinase-substrate phospho-site pairs are quantified in PhosphoNET. Kinexus Bioinformatics Corporation has the capability to test most of these putative interactions in vitro for our clients.

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• SciCrunch
• 16 years ago - by Anonymous

Bioinformatics Perl extension for the analysis of antibody variable domain repertoires.

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• SciCrunch
• 13 years ago - by Anonymous

A pipeline for assembling DNA sequence data generated on the Illumina sequencing platform.

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• SciCrunch
• 13 years ago - by Anonymous

A collection of tools and class interfaces for the assembly of DNA reads.

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• SciCrunch
• 13 years ago - by Anonymous

A Hadoop based genome assembler for assembling large genomes in the clouds.

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• SciCrunch
• 13 years ago - by Anonymous

Software providing a method that automatically determines suited overlaps cutoffs according to the contextual coverage, reducing thus the need for manual parameterization.

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• SciCrunch
• 13 years ago - by Anonymous

A software to assemble short reads of next generation sequencing technologies at low coverage.

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• SciCrunch
• 13 years ago - by Anonymous

Software for a de novo genome assembler implemented in C++.

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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

Site for collection and distribution of clinical data related to genetic analysis of drug abuse phenotypes. Anonymous data on family structure, age, sex, clinical status, and diagnosis, DNA samples and cell line cultures, and data derived from genotyping and other genetic analyses of these clinical data and biomaterials, are distributed to qualified researchers studying genetics of mental disorders and other complex diseases at recognized biomedical research facilities. Phenotypic and Genetic data will be made available to general public on release dates through distribution mechanisms specified on website.

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• SciCrunch
• 17 years ago - by Anonymous

A genetic sequence assembler capable of assembling millions of small nucleotide reads even in the presence of sequencing error.

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• SciCrunch
• 13 years ago - by Anonymous

Software for a probabilistic framework for the discovery of single nucleotide variants in WGSS data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 13 years ago - by Anonymous

A web-based GUI distributed computational pipeline, provides all-in-one functionality including human transcriptome quantification and the typical endogenous RNA-Sequencing analysis along with the investigation of exogenous sequences.

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• SciCrunch
• 13 years ago - by Anonymous

Commercial neuroimaging software package for multi-modal data analysis and management. It has been programmed in C++ with efficient statistical, numerical, and image processing routines. It supports parallelized basic math routines on all platforms and uses modern multi-core, multi-processor hardware for demanding computational routines.

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• SciCrunch
• 17 years ago - by Anonymous

A computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression of eukaryotes, prokaryotes, as well as organisms with no available genome reference sequence.

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• SciCrunch
• 13 years ago - by Anonymous

A computer program for phasing observed genotypes and imputing missing genotypes.

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• SciCrunch
• 13 years ago - by Anonymous

A fast and sensitive variant-caller for inferring single-nucleotide variants (SNVs) from high-throughput sequencing data.

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• SciCrunch
• 13 years ago - by Anonymous

A software tool for prioritizing candidate variants in family-based studies of inherited disease.

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• SciCrunch
• 13 years ago - by Anonymous

A suite of software tools that enables integrative SNP analysis in next generation sequencing data with large cohorts.

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• SciCrunch
• 13 years ago - by Anonymous