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http://www.ncbi.nlm.nih.gov/homologene

Automated system for constructing putative homology groups from complete gene sets of wide range of eukaryotic species. Databse that provides system for automatic detection of homologs, including paralogs and orthologs, among annotated genes of sequenced eukaryotic genomes. HomoloGene processing uses proteins from input organisms to compare and sequence homologs, mapping back to corresponding DNA sequences. Reports include homology and phenotype information drawn from Online Mendelian Inheritance in Man, Mouse Genome Informatics, Zebrafish Information Network, Saccharomyces Genome Database and FlyBase.

Proper citation: HomoloGene (RRID:SCR_002924) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/mapview/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023. Database that provides special browsing capabilities for a subset of organisms in Entrez Genomes. Map Viewer allows users to view and search an organism's complete genome, display chromosome maps, and zoom into progressively greater levels of detail, down to the sequence data for a region of interest. If multiple maps are available for a chromosome, it displays them aligned to each other based on shared marker and gene names, and, for the sequence maps, based on a common sequence coordinate system.

Proper citation: MapViewer (RRID:SCR_003092) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/tools/epcr/

Web tool that identifies sequence tagged sites (STSs) within DNA sequences. Using e-PCR, you can search for sub-sequences that closely match the PCR primers and have the correct order, orientation, and spacing. The software may also be downloaded to run locally.

Proper citation: e-PCR (RRID:SCR_003082) Copy   

•   Source: SciCrunch Registry

http://biocomputer.bio.cuhk.edu.hk/T3DB/

Database aimed to annotate all bacterial Type III Secretion System (T3SS) related structure, effector, regulator, and auxiliary genes.

Proper citation: Type-III-Secretion-System related database (RRID:SCR_002941) Copy   

•   Source: SciCrunch Registry

http://linux1.softberry.com/berry.phtml?topic=plantprom&group=data&subgroup=plantprom

Annotated, non-redundant database of proximal promoter sequences for RNA polymerase II with experimentally determined transcription start site(s) (TSS) from various plant species. It contains 578 unrelated entries including 151, 396 and 31 promoters with experimentally verified TSS from monocot, dicot and other plants, respectively (April 2014). This DB presents the published promoter sequences with TSS(s) determined by direct experimental approaches and therefore serves as the most accurate source for development of computational promoter prediction tools.

Proper citation: PlantProm DB (RRID:SCR_003359) Copy   

•   Source: SciCrunch Registry

http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/index.cgi

A plant promoter database that provides information on transcription start sites (TSSs), core promoter structure and regulatory element groups (REGs) as putative and comprehensive transcriptional regulatory elements. Microarray data-based predictions have been appended as REG annotations which inform their putative physiological roles.

Proper citation: PPDB: Plant Promoter Database (RRID:SCR_003395) Copy   

•   Source: SciCrunch Registry

http://cbdm.mdc-berlin.de/~amer/cgi-bin/nyce

Data analysis service that predicts subcellular location (either Nuclear, Nucleo-cytoplasmic, Cytoplasmic or Extracellular) of eukaryotic proteins using the predicted exposure value of their amino acids.

Proper citation: NYCE (RRID:SCR_003144) Copy   

•   Source: SciCrunch Registry

http://babelomics.bioinfo.cipf.es

An integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Version 4 of Babelomics integrates primary (normalization, calls, etc.) and secondary (signatures, predictors, associations, TDTs, clustering, etc.) analysis tools within an environment that allows relating genomic data and/or interpreting them by means of different functional enrichment or gene set methods. Such interpretation is made not only using functional definitions (GO, KEGG, Biocarta, etc.) but also regulatory information (from Transfac, Jaspar, etc.) and other levels of regulation such as miRNA-mediated interference, protein-protein interactions, text-mining module definitions and the possibility of producing de novo annotations through the Blast2GO system . Babelomics has been extensively re-engineered and now it includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. In this release GEPAS and Babelomics have integrated into a unique web application with many new features and improvements: * Data input: import and quality control for the most common microarray formats * Normalization and base calling: for the most common expression, tiling and SNP microarrays (Affymetrix and Agilent). * Transcriptomics: diverse analysis options that include well established as well as novel algorithms for normalization, gene selection, class prediction, clustering and time-series analysis. * Genotyping: stratification analysis, association, TDT. * Functional profiling: functional enrichment and gene set enrichment analysis with functional terms (GO, KEGG, Biocarta, etc.), regulatory (Transfac, Jaspar, miRNAs, etc.), text-mining, derived bioentities, protein-protein interaction analysis. * Integrative analysis: Different variables can be related to each other (e.g. gene expression to gnomic copy number) and the results subjected to functional analysis. Platform: Online tool

Proper citation: Babelomics (RRID:SCR_002969) Copy   

•   Source: SciCrunch Registry

https://netbio.bgu.ac.il/labwebsite/software/responsenet/

WebServer that identifies high-probability signaling and regulatory paths that connect input data sets. The input includes two weighted lists of condition-related proteins and genes, such as a set of disease-associated proteins and a set of differentially expressed disease genes, and a molecular interaction network (i.e., interactome). The output is a sparse, high-probability interactome sub-network connecting the two sets that is biased toward signaling pathways. This sub-network exposes additional proteins that are potentially involved in the studied condition and their likely modes of action. Computationally, it is formulated as a minimum-cost flow optimization problem that is solved using linear programming.

Proper citation: ResponseNet (RRID:SCR_003176) Copy   

•   Source: SciCrunch Registry

http://www.jci-bioinfo.cn/iLoc-Animal

Data analysis service for predicting subcellular localization of animal proteins with single or multiple sites.

Proper citation: iLoc-Animal (RRID:SCR_003173) Copy   

•   Source: SciCrunch Registry

https://www.hsph.harvard.edu/alkes-price/software/

Software application that uses genotyping data from SNP arrays for accurately inferring chromosomal segments of distinct continental ancestry in admixed populations, using dense genetic data. (entry from Genetic Analysis Software)

Proper citation: Hapmix (RRID:SCR_004203) Copy   

•   Source: SciCrunch Registry

http://www.biocomputing.it/fidea/

A web server for the functional interpretation of differential expression analysis. It can: * Calculate overrepresentation statistics using KEGG, Interpro, Gene Ontology Molecular Function, Gene Ontology Biological Process, Gene Ontology Cellular Component and GoSlim classifications; * Analyze down-regulated and up-regulated DE genes separately or together as a single set; * Provide interactive graphs and tables that can be modified on the fly according to user defined parameters; the user can set a fold change filter and interactively see the effects on the gene set under examination; * Output publication-ready plot of the graph; * Compare the results of several experiments in any combination.

Proper citation: FIDEA (RRID:SCR_004187) Copy   

•   Source: SciCrunch Registry

http://www.factorbook.org/

A Wiki-based database for transcription factor-binding data generated by the ENCODE consortium.

Proper citation: Factorbook (RRID:SCR_004086) Copy   

•   Source: SciCrunch Registry

http://www.mycancergenome.org/

A freely available online personalized cancer medicine knowledge resource for physicians, patients, caregivers and researchers that gives up-to-date information on what mutations make cancers grow and related therapeutic implications, including available clinical trials. It is a one-stop tool that matches tumor mutations to therapies, making information accessible and convenient for busy clinicians.

Proper citation: My Cancer Genome (RRID:SCR_004140) Copy   

•   Source: SciCrunch Registry

http://tools.niehs.nih.gov/polg/

Database that lists all known mutations in the coding region of the POLG gene and describes the associated disease. Human DNA polymerase is composed of two subunits, a 140 kDa catalytic subunit encoded by the POLG on chromosome 15q25, and a 55kDa accessory subunit encoded by the POLG2 gene on chromosome 17q23-24. A number of mutations have been mapped to the gene for the catalytic subunit of DNA polymerase, POLG, and found to be associated with mitochondrial diseases. The nucleotide changes are numbered from the initiation Methionine codon and are based on the cDNA (accession U60325.1) and gene sequence (accession AF497906.1).

Proper citation: Human DNA Polymerase Gamma Mutation Database (RRID:SCR_004722) Copy   

•   Source: SciCrunch Registry

http://bioinfo.au.tsinghua.edu.cn/nu_oscar/oscar.html

Software tool to identify binding sites of known transcription factors on promoter regions. The algorithm is based on one-class support vector machine (One-class SVM). OSCAR uses the sequential composition of known binding sites, and further incorporates the locational preferences of binding events. Nu-OSCAR (Nucleosome-Occupancy Study for Cis-elments Accurate Recognition) is a program that can be used to identify binding sites of known transcription factors, which further incorporates nucleosome occupancy around sites on promoter regions, thereby improving the accuracy of prediction. The derivation of the the algorithm is based on a biophysical view of interactions between protein factors and nucleosome DNA.

Proper citation: Nu-OSCAR (RRID:SCR_004513) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/unigene

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Web tool for an organized view of the transcriptome. Collection of the computationally identified transcripts from the same locus. Information on protein similarities, gene expression, cDNA clones, and genomic location. System for automatically partitioning GenBank sequences into a non redundant set of gene oriented clusters.

Proper citation: UniGene (RRID:SCR_004405) Copy   

•   Source: SciCrunch Registry

http://www.genengnews.com/keyword/next-generation-sequencing/231

News source including the entire bioproduct life cycle from early-stage R&D, to applied research including omics, biomarkers, as well as diagnostics, to bioprocessing and commercialization.

Proper citation: GEN (RRID:SCR_012901) Copy   

•   Source: SciCrunch Registry

http://www.mothur.org/

An open-source software package for describing and comparing microbial communities. It incorporates the functionality of a number of computational tools, calculators, and visualization tools.

Proper citation: mothur (RRID:SCR_011947) Copy   

•   Source: SciCrunch Registry

http://www.bikalabs.com/

Open Source laboratory information management systems.

Proper citation: BIKA (RRID:SCR_011828) Copy   

•   Source: SciCrunch Registry