Curator Dashboard

Software that detects and quantifies short IN/DELs as well as single nucleotide substitutions in pooled-DNA samples.

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• SciCrunch
• 13 years ago - by Anonymous

Web server that summarizes lists of Gene Ontology terms by removing redundant terms and visualizing the remaining ones in scatterplots, interactive graphs, treemaps, or tag clouds. Platform: Online tool, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 15 years ago - by Anonymous

A text processing system that allows you to do textmining tasks on text. It is great at identifying molecular biology terms and linking them to publicly available databases. Whatizit is also a Medline abstracts retrieval/search engine. Instead of providing the text by Copy&Paste, you can launch a Medline search. The abstracts that match your search criteria are retrieved and processed by a pipeline of your choice. Whatizit is also available as 1) a webservice and as 2) a streamed servlet. The webservice allows you to enrich content within your website in a similar way as in the wikipedia. The streamed servlet allows you to process large amounts of text.

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• SciCrunch
• 15 years ago - by Anonymous

A web server which allows users to explore PubMed search results with the Gene Ontology, a hierarchically structured vocabulary for molecular biology. GoPubMed submits a user''''s keywords to PubMed, retrieves the abstracts, detects Gene Ontology terms in the abstracts, displays the subset of Gene Ontology relevant to the original query, and allows the user to browse through the ontology displaying associated papers and their GO annotation. Platform: Online tool

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• SciCrunch
• 15 years ago - by Anonymous

GOChase is a set of web-based utilities to detect and correct the errors in GO-based annotations. # GOChase-History resolves the whole modification history of GO IDs. # GOChase-Correct highlights merged GO IDs and redirects to the correct primary term into which the secondary ID was merged. For obsolete GO terms, the nearest non-discarded parent term is recommended by GOChase. This function may be used by GO browsers such as AmiGO and QuickGO to fix broken hyperlinks. # A whole database (such as LocusLink) as a flat file can be loaded into GOChase, reporting the annotation errors and GOChase corrections. # When one inputs a GO ID, GOChase will resolve all gene products annotated with the GO ID across all the major databases. Platform: Online tool

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• SciCrunch
• 15 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The EP:GO browser is built into EBI's Expression Profiler, a set of tools for clustering, analysis and visualization of gene expression and other genomic data. With it, you can search for GO terms and identify gene associations for a node, with or without associated subnodes, for the organism of your choice.

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• SciCrunch
• 15 years ago - by Anonymous

A Galaxy framework-based online pipeline for reliable analysis of data generated by three types of CLIP-seq protocols: HITS-CLIP, PAR-CLIP and iCLIP. It provides both data processing and statistical analysis to determine candidate cross-linking regions, which are comparable to those regions identified from the original studies or using existing computational tools., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 13 years ago - by Anonymous

The Functional Similarity Search Tool (FSST) has been implemented for comparing user defined sets of annotated entities. FSST supports the computation of functional similarity scores based on an individual ontology and of combined scores. Its multi-threaded Java implementation takes advantage of symmetric multi-processing computers, decreasing runtime considerably. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

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• SciCrunch
• 15 years ago - by Anonymous

Database that contains publicly available protein sequences with stable and unique identifiers (UPI) which are never removed, changed or reassigned. UniParc tracks sequence changes in the source databases and archives the history of all changes. Information other than protein sequence must be retrieved from the UniParc source databases using the database cross-references.

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• SciCrunch
• 17 years ago - by Anonymous

An integrated database of human maladies and their annotations, modeled on the architecture and richness of the popular GeneCards database of human genes. The database contains 17,705 diseases, consolidated from 28 sources.

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• SciCrunch
• 15 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 2,2025. G-SESAME contains a set of tools. They include: tools for measuring the semantic similarity of GO terms; tools for measuring the functional similarity of genes; and tools for clustering genes based on their GO term annotation information. Platform: Online tool, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 15 years ago - by Anonymous

The Integrated Tool for IC-based GO Semantic Similarity Measures (IT-GOM) integrates the currently known GO semantic similarity measures into a single tool. It provides the information content (IC) of GO terms, semantic similarity between GO terms and GO-based protein functional similarity scores. The specificity of GO terms and the similarity of biological content between GO terms or proteins are transformed into numeric values for protein analyses at the functional level. The integration of the different measures enables users to choose the measure best suited to their application and to compare results between different semantic similarity measures. Platform: Online tool

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• SciCrunch
• 15 years ago - by Anonymous

An Antibody supplier

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• SciCrunch
• 14 years ago - by Anonymous

GO-Module provides an interface to reduce the dimensionality of GO enrichment results and produce interpretable biomodules of significant GO terms organized by hierarchical knowledge that contain only true positive results. Users can download a text file of GO terms annotated with their significance and identified biomodules, a network visualization of resultant GO IDs or terms in PDF format, and view results in an online table. Platform: Online tool

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• SciCrunch
• 15 years ago - by Anonymous

TXTGate is a literature index database and is part of an experimental platform to evaluate (combinations of) information extraction and indexing from a variety of biological annotation databases. It is designed towards the summarization and analysis of groups of genes based on text. By means of tailored vocabularies, selected textual fields and MedLine abstracts of LocusLink and SGD are indexed. Subclustering and links to external resources allow for an in-depth analysis of the resulting term profiles. You need to be registered in order to use the TXTGate application. Platform: Online tool

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• SciCrunch
• 15 years ago - by Anonymous

A program specifically designed for de novo spliced mapping of mRNA-seq reads. It adopts a multiple-seed-and-extend scheme, and does not rely on a separate external mapper.

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• SciCrunch
• 13 years ago - by Anonymous

BrainStars (or B*) is a quantitative expression database of the adult mouse brain. The database has genome-wide expression profile at 51 adult mouse CNS regions. For 51 CNS regions, slices (0.5-mm thick) of mouse brain were cut on a Mouse Brain Matrix, frozen, and the specific regions were punched out bilaterally with a microdissecting needle (gauge 0.5 mm) under a stereomicroscope. For each region, we took samples every 4 hours, starting at ZT0 (Zeitgaber time 0; the time of lights on), for 24 hours (6 time-point samples for each region), and we pooled the samples from the different time points. We independently sampled each region twice (n=2). These samples were purified their RNA, and measured with Affymetrix GeneChip Mouse Genome 430 2.0 arrays. Expression values were then summarized with the RMA method. After several analysis with the expression data, the data and analysis results were stored in the BrainStars database. The database has a REST-like Web API interface for accessing from your Web applications. This document shows how to access the database via our Web API.

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• SciCrunch
• 15 years ago - by Anonymous

A knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. BiGG integrates several published genome-scale metabolic networks into one resource with standard nomenclature which allows components to be compared across different organisms. BiGG can be used to browse model content, visualize metabolic pathway maps, and export SBML files of the models for further analysis by external software packages. Users may follow links from BiGG to several external databases to obtain additional information on genes, proteins, reactions, metabolites and citations of interest.

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• SciCrunch
• 15 years ago - by Anonymous

GoBean is a Java application for gene ontology enrichment analysis. It utilizes the NetBeans platform framework. Features * Graphical comparison of multiple enrichment analysis results * Versatile filter facility for focused analysis of enrichment results * Effective exploitation of the graphical/hierarchical structure of GO * Evidence code based association filtering * Supports local data files such as the ontology obo file and gene association files * Supports late enrichment methods and multiple testing corrections * Built-in ID conversion for common species using Ensembl biomart service Platform: Windows compatible, Mac OS X compatible, Linux compatible

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• SciCrunch
• 15 years ago - by Anonymous

Data analysis service that predicts functions of cis-regulatory regions identified by localized measurements of DNA binding events across an entire genome. Whereas previous methods took into account only binding proximal to genes, GREAT is able to properly incorporate distal binding sites and control for false positives using a binomial test over the input genomic regions. GREAT incorporates annotations from 20 ontologies and is available as a web application. The utility of GREAT extends to data generated for transcription-associated factors, open chromatin, localized epigenomic markers and similar functional data sets, and comparative genomics sets. Platform: Online tool

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• SciCrunch
• 15 years ago - by Anonymous