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on page 1 showing 20 out of 693 results from 1 sources

Cite this (3D-Interologs, RRID:SCR_003101)

URL: http://gemdock.life.nctu.edu.tw/3D-Interologs

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resource

Database of physical protein-protein interactions across multiple genomes. Based on 3D-domain interolog mapping and a scoring function, protein-protein interactions are inferred by using three-dimensional (3D) structure heterodimers to search the UniProt database. For a query protein, the database utilizes BLAST to identify homologous proteins and the interacting partners from multiple species. Based on the scoring function and structure complexes, it provides the statistic significances, the interacting models (e.g. hydrogen bonds and conserved amino acids), and functional annotations of interacting partners of a query protein. The identification of orthologous proteins of multiple species allows the study of protein-protein evolution, protein functions, and cross-referencing of proteins.

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    ADaCGH

Cite this (ADaCGH, RRID:SCR_010916)

URL: http://adacgh.bioinfo.cnio.es/

Resource Type: Resource, analysis service resource, software resource, data analysis service, service resource, production service resource

A web tool for the analysis of aCGH data sets. They focus on calling gains and losses and estimating the number of copy changes. Note: ADaCGH will continue being maintained, but is deprecated. Their new tool for CGH and CNV is WaviCGH, http://wavi.bioinfo.cnio.es/

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Cite this (ADDA - Automatic Domain Decomposition Algorithm, RRID:SCR_007546)

URL: http://ekhidna.biocenter.helsinki.fi/sqgraph/pairsdb

Resource Type: Resource, data analysis service, database, analysis service resource, production service resource, service resource, data or information resource

This is a web interface for ADDA, an automatic algorithm for domain decomposition and clustering of all protein domain families. We use alignments derived from an all-on-all sequence comparison to define domains within protein sequences based on a global maximum likelihood model. ADDA is downloadable. There are three ways in which you can retrieve a protein sequence and its domains from ADDA. Sequences can be located using sequence identifiers and/or accession numbers, using a identical fragment lookup, or by running BLAST against all sequences in ADDA. ADDA is a protein sequence clustering algorithm. It takes a set of sequences and returns domain families. ADDA has two steps corresponding to the two aspects of the protein sequence clustering domain. First, ADDA splits protein sequences into domains. The idea behind ADDA is in principle the application of Occam''s razor; the goal is to describe the diversity of protein sequences with a minimal set of protein domains. The algorithm behind ADDA approximates this minimal set. In practice ADDA works by looking at where BLAST alignments are located on the sequence and splits the sequences, so that as few as possible alignments are cut by domain boundaries and that as many alignments as possible stretch over complete domains. Secondly, ADDA takes all the domains and then arranges them in a minimum spanning tree, where the similarity between two domains is determined by their relative overlap given a BLAST alignment. Each link in the tree is then checked by a pairwise profile-profile comparison and links below a threshold are removed. The remaining connected components are then taken to represent protein domain families.

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    ADGO

Cite this (ADGO, RRID:SCR_006343)

URL: http://www.btool.org/ADGO2

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

A web-based tool that provides composite interpretations for microarray data comparing two sample groups as well as lists of genes from diverse sources of biological information. It provides multiple gene set analysis methods for microarray inputs as well as enrichment analyses for lists of genes. It screens redundant composite annotations when generating and prioritizing them. It also incorporates union and subtracted sets as well as intersection sets. Users can upload their gene sets (e.g. predicted miRNA targets) to generate and analyze new composite sets.

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Cite this (Aggrescan: The Hot Spot Finder, RRID:SCR_008403)

URL: http://bioinf.uab.es/aggrescan/

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

Web-based tool for identifying hot spots of aggregation in polypeptides. Aggrescan uses an aggregation-propensity scale for natural amino acids derived from in vivo experiments and on the assumption that short and specific sequence stretches modulate protein aggregation. The algorithm is shown to identify a series of protein fragments involved in the aggregation of disease-related proteins and to predict the effect of genetic mutations on their deposition propensities. It also provides new insights into the differential aggregation properties displayed by globular proteins, natively unfolded polypeptides, amyloidogenic proteins and proteins found in bacterial inclusion bodies.

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    agriGO

Cite this (agriGO, RRID:SCR_006989)

URL: http://bioinfo.cau.edu.cn/agriGO/

Resource Type: Resource, data analysis service, database, analysis service resource, production service resource, service resource, data or information resource

A web-based tool and database for the gene ontology analysis. Its focus is on agricultural species and is user-friendly. The agriGO is designed to provide deep support to agricultural community in the realm of ontology analysis. Compared to other available GO analysis tools, unique advantages and features of agriGO are: # The agriGO especially focuses on agricultural species. It supports 45 species and 292 datatypes currently. And agriGO is designed as an user-friendly web server. # New tools including PAGE (Parametric Analysis of Gene set Enrichment), BLAST4ID (Transfer IDs by BLAST) and SEACOMPARE (Cross comparison of SEA) were developed. The arrival of these tools provides users with possibilities for data mining and systematic result exploration and will allow better data analysis and interpretation. # The exploratory capability and result visualization are enhanced. Results are provided in different formats: HTML tables, tabulated text files, hierarchical tree graphs, and flash bar graphs. # In agriGO, PAGE and SEACOMPARE can be used to carry out cross-comparisons of results derived from different data sets, which is very important when studying multiple groups of experiments, such as in time-course research. Platform: Online tool

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Cite this (Algal Functional Annotation Tool, RRID:SCR_012034)

URL: http://pathways.mcdb.ucla.edu/algal/

Resource Type: Resource, data analysis service, database, analysis service resource, production service resource, service resource, data or information resource

Tools to search gene lists for functional term enrichment as well as to dynamically visualize proteins onto pathway maps. Additionally, integrated expression data may be used to discover similarly expressed genes based on a starting gene of interest.

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Cite this (Align-GVGD, RRID:SCR_010772)

URL: http://agvgd.iarc.fr/index.php

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

A freely available, web-based program that combines the biophysical characteristics of amino acids and protein multiple sequence alignments to predict where missense substitutions in genes of interest fall in a spectrum from enriched delterious to enriched neutral.

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    ALLELIX

Cite this (ALLELIX, RRID:SCR_009115)

URL: http://www.allelix.net

Resource Type: Resource, data analysis service, production service resource, analysis service resource, software application, service resource, software resource

THIS RESOURCE IS NO LONGER IN SERVICE, documented on September 23, 2013. Software application / data analysis service where one can enter the alleles of commonly used STR by clicking the mouse. The algorithm calculates the paternity index and the Essen-Moeller probability of kinship for the deficiency- and the trio case. Everybody can use the network-software online after registering. The usage on the internet is free. Academic users can ask me to unlock an option to display the details (formulas/frequencies etc.) and to have an export-funktion to MS Word. The program is in German and (non-professional) English. An expansion to other languages is easy, if somebody helps us with the translation. For those who are interested to have the software running on their own intranet (for database security reasons) an individual agreement can be found. (entry from Genetic Analysis Software) (German version is: http://www.allelix.de)

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Cite this (AllerHunter: Cross-reactive Allergen Prediction Home, RRID:SCR_002950)

URL: http://tiger.dbs.nus.edu.sg/AllerHunter

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

A cross-reactive allergen prediction program built on a combination of Support Vector Machine (SVM) and pairwise sequence similarity. Cross-reactivity is based on similarity of proteins to allergens. However, not all proteins with similar sequence or structure to known allergens are cross-reactive allergens. AllerHunter aims to predict allergens and non-allergens with high sensitivity and specificity, without compromising efficiency at classification of proteins with similar sequence to known allergens. There are distinct differences between prediction of allergenicity and cross-reactivity of allergens. Allergenicity is the immunogenic potential of an allergen to induce IgE antibody production, whereas cross-reactivity is the potential of a substance to bind to IgE previously induced by a known allergen. It is difficult to predict allergenicity because causes of immunogenicity of allergens are still not completely clear. However it is possible to predict cross-reactivity since it implies similarity in IgE binding sites. Please provide protein sequence in fasta format.

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    AmiGO

Cite this (AmiGO, RRID:SCR_002143)

URL: http://amigo.geneontology.org/

Resource Type: Resource, data analysis service, database, analysis service resource, software application, production service resource, service resource, software resource, data or information resource

Official Web-based tools for searching and browsing the Gene Ontology database, which consists of a controlled vocabulary of terms covering biological concepts, and a large number of genes or gene products whose attributes have been annotated using GO terms. It can be accessed online at the main installation or deployed locally. The Gene Ontology project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases. AmiGO can be used to:
* search for a gene or gene product, or a list of gene or gene products, and view the GO term associations
* perform a sequence identity BLAST search and view the GO term associations for the genes or proteins returned
* search for GO terms and view the genes or gene products they are annotated to
* browse the GO ontology and view terms
* the slimmer tool can be used to map the granular annotations of the query set of genes to one or more high-level
* term enrichment tool is used to discover what a set of genes may have in common by examining annotations and finding significant shared GO terms.
* GOOSE is for advanced users who want to run custom SQL queries against the GO database.

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Cite this (AmphoraNet, RRID:SCR_005009)

URL: http://amphoranet.pitgroup.org/

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

Webserver implementation of the AMPHORA2 workflow for phylogenetic analysis of metagenomic shotgun sequencing data. It is capable of assigning a probability-weighted taxonomic group for each phylogenetic marker gene found in the input metagenomic sample.

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Cite this (AMYL-PRED, RRID:SCR_006185)

URL: http://bioinformatics.biol.uoa.gr/AMYLPRED/

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

A web tool using the consensus prediction method for identifying possible amyloidogenic regions in protein sequences. This tool uses an assortment of different methods that have been found or specifically developed to predict features related to the formation of amyloid fibrils. The consensus of these methods is defined as the the hit overlap of at least two out of five methods and it is the primary output of the program. However, the individual predictions of these methods are also made available in the form of a text file, maintained on the server for 1 (one) day. Consequently, the tool predicts probable amyloidogenic determinants for a given amino acid sequence of a peptide or protein.

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    Ancora

Cite this (Ancora, RRID:SCR_001623)

URL: http://ancora.genereg.net/

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resource

Web resource that provides data and tools for exploring genomic organization of highly conserved noncoding elements (HCNEs) for multiple genomes. It includes a genome browser that shows HCNE locations and features novel HCNE density plots as a powerful tool to discover developmental regulatory genes and distinguish their regulatory elements and domains. They identify HCNEs as non-exonic regions of high similarity between genome sequences from distantly related organisms, such as human and fish, and provide tools for studying the distribution of HCNEs along chromosomes. Major peaks of HCNE density along chromosomes most often coincide with developmental regulatory genes. Their aim with this site is to aid discovery of developmental regulatory genes, their regulatory domains and their fundamental regulatory elements.

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    aneurIST

Cite this (aneurIST, RRID:SCR_007427)

URL: http://www.aneurist.org/

Resource Type: Resource, topical portal, production service resource, analysis service resource, data analysis service, standard specification, narrative resource, service resource, portal, knowledge environment, data or information resource

An IT infrastructure for the management, integration and processing of data associated with the diagnosis and treatment of cerebral aneurysm and subarachnoid hemorrhage. This new paradigm to understand and manage cerebral aneurysms, provides an integrated decision support system to assess the risk of aneurysm rupture in patients and to optimize their treatments. aneurIST benefits patients with better diagnostics, prevention and treatment because it combines efforts of clinicians and industry. Through research clinicians gain a greater insight in aneurysm understanding, while industry will be dragged by these achievements to develop more suitable medical devices to treat the disease. This infrastructure : * Facilitate clinicians the diagnosis and study of the disease, as a result of providing a seamless access to patient data using data fusion and processing of complex information spanning from the molecular to the personal level. * Provide a better planning and personalization of minimally invasive interventional procedures for patients, after linking modern diagnostic imaging to computational tools. * Collaborate in the development, extension and exploitation of standards and protocols at all project stages. * Share biomedical knowledge providing access to a set of software tools and platforms such as aneuLink, aneuFuse, aneuRisk, aneuEndo, aneuCompute and aneuInfo. * Create awareness through scientific dissemination and collaboration. * Explore the business opportunities directly arising from aneurIST. It intends to provide an integrated decision support system to assess the risk of aneurysm rupture in patients and to optimize their treatments. Software: * aneuLink will create an IT environment with the goal of establishing a link between genomics and disease. * aneuFuse will fuse diagnostic, modelling and simulation data into a coherent representation of the patient''s condition. * aneuRisk will provide clinicians with a tool to facilitate the personalized risk assessment and guidelines establishment to treat patients. * aneuEndo will develop computational tools to optimize and customize the design of endovascular devices. * aneuInfo will enable access to clinical and epidemiological data distributed in public and project-specific protected databases. * aneuCompute will provide aneurIST with distributed computing capabilities ensuring secure data transport.

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Cite this (APHIDBASE, RRID:SCR_001765)

URL: http://www.aphidbase.com/aphidbase/

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resource

Centralized bioinformatic resource that facilitates community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). It aims to (i) store recently acquired genomic resources on aphids and (ii) compare them to other insect resources as functional annotation tools. The AphidBase Information System designed to organize and distribute genomic data and annotations for a large international community was constructed using open source software tools from the Generic Model Organism Database (GMOD). The system includes Apollo and GBrowse utilities as well as a wiki, blast search capabilities and a full text search engine. For that, the Drosophila melanogaster genome has been loaded in the database using the GMOD open source software for a comparison with the 17 069 pea aphid unique transcripts (contigs) and the 13 639 gene transcripts of the Anopheles gambiae. Links to FlyBase and A.gambiae Entrez databases allow a rapid characterization of the putative functions of the aphid sequences. Text mining of the D.melanogaster literature was performed to construct a network of co-cited gene or protein names, which should facilitate functional annotation of aphid homolog sequences. AphidBase represents one of the first genomic databases for a hemipteran insect.

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Cite this (APID: Agile Protein Interaction DataAnalyzer, RRID:SCR_008871)

URL: http://bioinfow.dep.usal.es/apid

Resource Type: Resource, data analysis service, database, analysis service resource, production service resource, service resource, data or information resource

An interactive bioinformatics web tool developed to integrate and analyze in a unified and comparative platform known information about protein-protein interactions demonstrated by specific small-scale or large-scale experimental methods. At present, the application includes information coming from five main source databases enclosing an unified sever to explore more than 40000 different proteins and close to 150000 different proven interactions. The website includes search tools to query and browse upon the data, allowing selection of the interaction pairs based in calculated parameters that weight and qualify the reliability of each given protein interaction. Parameters for the proteins are connectivity, cluster coefficient, Gene Ontology (GO) functional environment, GO environment enrichment; for the interactions: number of methods, GO overlapping, Pfam domain-domain interaction. APID also includes a graphic interactive tool to visualize selected sub-networks and to navigate on them or along the whole interaction network. Platform: Online tool

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Cite this (ApiDB PlasmoDB, RRID:SCR_013331)

URL: http://PlasmoDB.org

Resource Type: Resource, data analysis service, data access protocol, production service resource, analysis service resource, database, web service, service resource, software resource, data or information resource

PlasmoDB is a genome database for the genus Plasmodium, a set of single-celled eukaryotic pathogens that cause human and animal diseases, including malaria. It brings together data provided by numerous laboratories worldwide (see the Data Sources page), and adds its own data analysis. PlasmoDB is a functional genomic database for Plasmodium spp. that provides a resource for data analysis and visualization in a gene-by-gene or genome-wide scale. PlasmoDB belongs to a family of genomic resources that are housed under the EuPathDB Bioinformatics Resource Center (BRC) umbrella. PlasmoDB contains numerous data types from several broad categories--annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution. Data in PlasmoDB can be queried by selecting the data of interest from a query grid or drop down menus. Various results can then be combined with each other on the query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis. Organisms * Annotated genomes: Plasmodium falciparum, Plasmodium vivax, Plasmodium yoelii, Plasmodium berghei, Plasmodium chabaudi, Plasmodium knowlesi * Unannotated genomes: Plasmodium reichenowi, Plasmodium gallinaceum * Others: environmental isolate sequences from numerous species PlasmoDB provides programmatic access to its searches, via REST Web Services.

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Cite this (Arabidopsis thaliana Genome Database, RRID:SCR_001901)

URL: http://www.plantgdb.org/AtGDB/

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resource

Database providing a sequence-centered genome view for Arabidopsis thaliana, with a narrow focus on gene structure annotation. The current genome assembly displayed at AtGDB is version TAIR9. Annotated gene models are TAIR10. They have mapped the complete set of 176,915 publicly available Arabidopsis EST sequences onto the Arabidopsis genome using GeneSeqer, a spliced alignment program incorporating sequence similarity and splice site scoring. About 96% of the available ESTs could be properly aligned with a genomic locus, with the remaining ESTs deriving from organelle genomes and non-Arabidopsis sources or displaying insufficient sequence quality for alignment. The mapping provides verified sets of EST clusters for evaluation of EST clustering programs. Analysis of the spliced alignments suggests corrections to current gene structure annotation and provides examples of alternative and non-canonical pre-mRNA splicing.

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    ARCHER

Cite this (ARCHER, RRID:SCR_015854)

URL: http://www.archer.ac.uk/

Resource Type: Resource, analysis service resource, data analysis service, service resource, computational hosting, production service resource

Supercomputing service located in the UK for researchers who study problems with a global impact. It is part of the PRACE initiative giving leading scientific users access to a European pool of supercomputers.

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