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http://biome.ewha.ac.kr:8080/GSEAWebApp/

An integrative platform for diverse types of gene set analysis with annotation network navigation. It includes tools for statistical analysis, visualization of annotation relationships, retrieval of genes from annotation database, and set operation for gene sets. In an effort to allow access to a full spectrum of amassed biological knowledge, they have integrated a variety of annotation data that include the GO, domain, disease, drug, chromosomal location, and custom-defined annotations. Diverse types of molecular networks (pathways, transcription and microRNA regulations, protein-protein interaction) are also included. The pair-wise relationship between annotation gene sets was calculated using kappa statistics. GARNET consists of three modules--gene set manager, gene set analysis and gene set retrieval, which are tightly integrated to provide virtually automatic analysis for gene sets. A dedicated viewer for annotation network has been developed to facilitate exploration of the related annotations.

Proper citation: GARNET (RRID:SCR_012033) Copy   

•   Source: SciCrunch Registry

https://applications.bhsai.org/quartetsdb/

A large-scale orthology database for prokaryotes and eukaryotes inferred by evolutionary evidence. Contnet includes orthology predictions among 1621 complete genomes (1365 bacterial, 92 archaeal, and 164 eukaryotic), covering >7 million proteins and 4 million pairwise orthologs; Orthologous groups, comprising >300000 groups of orthologous proteins and >236000 corresponding gene trees; and inparalog groups, comprising >500000 groups of inparalogs.

Proper citation: QuartetS-DB (RRID:SCR_011981) Copy   

•   Source: SciCrunch Registry

http://gexp.kaist.ac.kr/figs/

A web-based workbench to conveniently compare the classification performances of many different filter-based gene selection procedures. In addition to the commonly used filter metric-classifier combinations, user can test various additive methodological options by specification of only up- or down-regulated genes to select, applying feature discretization and adding feature vectors to make a new feature. Throughout the comprehensive comparisons, user can identify the best performing gene selection procedure and subsequent classification performance measured by .632+ bootstrap error estimation for the given binary (two-class) microarray data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: FiGS (RRID:SCR_012037) Copy   

•   Source: SciCrunch Registry

http://proteogenomics.musc.edu/ma/arrayQuest.php?page=home&act=manage

A web-accessible program for the analysis of DNA microarray data. ArrayQuest is designed to apply any type of DNA microarray analysis program executable on a Linux system (i.e., Bioconductor statistical and graphical methods written in R as well as BioPerl and C++ based scripts) to DNA microarray data stored in the MUSC DNA Microarray Database, the Gene Expression Omnibus (GEO) or in a password protected private database uploaded to the center point server. ArrayQuest analyses are performed on a computer cluster.

Proper citation: ArrayQuest (RRID:SCR_010935) Copy   

•   Source: SciCrunch Registry

http://gettinggeneticsdone.blogspot.fr/

Blog about getting Things Done in Genetics & Bioinformatics Research.

Proper citation: Getting Genetics Done (RRID:SCR_011989) Copy   

•   Source: SciCrunch Registry

http://koch.pathogenomics.ca/cgi-bin/pub/arraypipe.pl

A flexible tool for visualizing and analyzing your two-colour microarray slides.

Proper citation: ArrayPipe (RRID:SCR_010934) Copy   

•   Source: SciCrunch Registry

http://mail.nbfgr.res.in/fishmicrosat/

A microsatellite database of commercially important fishes and shellfishes of the Indian subcontinent.

Proper citation: FishMicrosat (RRID:SCR_013012) Copy   

•   Source: SciCrunch Registry

http://dm.postech.ac.kr/refmed/

Relevance Feedback Search Engine for PubMed. When a user enters a keyword in the search box, the PubMed search results will be returned. The user then specifies on a sample of results how much they are relevant to what she intends to find, for example, by specifying whether each article is high relevant, somewhat relevant, or not relevant. Once the user clicks Push Feedback button, the system learns a relevance function from the feedback and returns the top articles ranked highly according to the relevance function. The user can repeat the process until she gets satisfying results.

Proper citation: RefMED (RRID:SCR_011871) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.charite.de/supercyp/

Database that contains about 1,170 drugs, 2,785 Cytochrome-Drug interactions and about 1,200 alleles.

Proper citation: SuperCYP (RRID:SCR_011957) Copy   

•   Source: SciCrunch Registry

http://bitsandbugs.org/

This blog reflects the workings of a group of scientists working at the intersection of public health microbiology and bioinformatics.

Proper citation: Bits and Bugs (RRID:SCR_012012) Copy   

•   Source: SciCrunch Registry

http://toolkit.tuebingen.mpg.de/clubsubp

Data analysis service for cluster-based Subcellular localization prediction.

Proper citation: ClubSub-P (RRID:SCR_011969) Copy   

•   Source: SciCrunch Registry

http://www.urogene.org/methprimer/

A public database holding PCR primers for popular DNA methylation analysis methods to prevent time-consuming primer design and experimental optimisation.

Proper citation: methPrimerDB (RRID:SCR_012017) Copy   

•   Source: SciCrunch Registry

http://pdbtm.enzim.hu/

Comprehensive and continuously updated transmembrane protein database of the Protein Data Bank (PDB) created by scanning all PDB entries with the TMDET algorithm. Resource for transmembrane proteins and their structures., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PDBTM (RRID:SCR_011962) Copy   

•   Source: SciCrunch Registry

http://model.nmr.ru/preddimer/

Prediction tool to reconstruct putative dimer conformations for given sequences of transmembrane protein fragments, which are considered as ideal alpha-helices.

Proper citation: PREDDIMER (RRID:SCR_011963) Copy   

•   Source: SciCrunch Registry

http://tmdet.enzim.hu/

Web server for the detection of the transmembrane regions of membrane proteins using their 3D structure only.

Proper citation: TMDET (RRID:SCR_011964) Copy   

•   Source: SciCrunch Registry

http://gpcr.biocomp.unibo.it/bacello/

A predictor for the subcellular localization of proteins in eukaryotes that is based on a decision tree of several support vector machines (SVMs). It classifies up to four localizations for Fungi and Metazoan proteins and five localizations for Plant ones. BaCelLo's predictions are balanced among different classes and all the localizations are considered as equiprobable.

Proper citation: BaCelLo (RRID:SCR_011965) Copy   

•   Source: SciCrunch Registry

http://www.csbio.sjtu.edu.cn/bioinf/Cell-PLoc/

A package of web-servers for predicting subcellular localization of proteins in different organisms.

Proper citation: Cell-PLoc (RRID:SCR_011966) Copy   

•   Source: SciCrunch Registry

http://cello.life.nctu.edu.tw/

A subCELlular LOcalization predictor based on a multi-class support vector machine (SVM) classification system. CELLO uses 4 types of sequence coding schemes: the amino acid composition, the di-peptide composition, the partitioned amino acid composition and the sequence composition based on the physico-chemical properties of amino acids. They combine votes from these classifiers and use the jury votes to determine the final assignment.

Proper citation: CELLO (RRID:SCR_011968) Copy   

•   Source: SciCrunch Registry

http://www.syapse.com/

A platform and application suite for bringing together omics and clinical data.

Proper citation: Syapse (RRID:SCR_012023) Copy   

•   Source: SciCrunch Registry

http://www.antibodypedia.com/

Open-access database of antibodies against human proteins developed through collaboration between Antibodypedia AB and the Nature Publishing Group. It aims to provide the scientific community and antibody distributors alike with information on the effectiveness of specific antibodies in specific applications--to help scientists select the right antibody for the right application. Antibodypedia's mission is to promote the functional understanding of the human proteome and expedite analysis of potential biomarkers discovered through clinical efforts. To this end, they have developed an open-access, curated, searchable database containing annotated and scored affinity reagents to aid users in selecting antibodies tailored to specific biological and biomedical assays. They envisage Antibodypedia as a virtual repository of validated antibodies against all human, and ultimately most model-organism, proteins. Such a tool will be exploitable to identify affinity reagents to document protein expression patterns in normal and pathological states and to purify proteins alone and in complex for structural and functional analyses. They hope to promote characterization of the roles and interplay of proteins and complexes in human health and disease. They encourage commercial providers to submit information regarding their inventory of antibodies with links to quality control data. Independent users can submit their own application-specific experimental data using standard validation criteria (supportive or non-supportive) developed with the assistance of an international advisory board recruited from academic research institutions. Users can also comment on specific antibodies without submitting validation data.

Proper citation: Antibodypedia (RRID:SCR_012782) Copy   

•   Source: SciCrunch Registry