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http://www.mirtoolsgallery.org/miRToolsGallery/node/1055

Comprehensive resource of microRNA target predictions and expression profiles. Used for whole genome prediction of miRNA target genes. For each miRNA, target genes are selected on basis of sequence complementarity using position weighted local alignment algorithm, free energies of RNA-RNA duplexes, and conservation of target sites in related genomes. Provides information about set of genes potentially regulated by particular microRNA, co-occurrence of predicted target sites for multiple microRNAs in mRNA and microRNA expression profiles in tissues. Users are allowed to customize algorithm, numerical parameters, and position-specific rules., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: miRanda (RRID:SCR_017496) Copy   

•   Source: SciCrunch Registry

http://www.clcbio.com/products/clc-main-workbench/

A suite of software for DNA, RNA and protein sequence data analysis. The software allows for the analysis and visualization of Sanger sequencing data as well as gene expression analysis, molecular cloning, primer design, phylogenetic analyses, and sequence data management.

Proper citation: CLC Main Workbench (RRID:SCR_000354) Copy   

•   Source: SciCrunch Registry

http://www.dnastar.com/t-genvision.aspx

A genomic visualization application to support easy generation of publication quality graphics and maps. It produces high quality images of annotated genomes but it can also be customized to accentuate specific areas of interest, such as comparing gene functionality, illustrating gene expression levels, and visualizing the coverage in an assembled contig.

Proper citation: GenVision (RRID:SCR_001166) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.udel.edu/Research/skategenomeproject

Core facility provides a model for collaborative approaches to use specialized resources and expertise in an integrated process. Core builds on the expertise and resources provided by the Bioinformatics Cores of the five northeastern states that form NECC. The Skate Genome Annotation Workshops and Jamborees offer training and opportunities for faculty and students to work with and annotate genome sequences. Workshops include lectures, tutorials and exercises annotating the genome of the little skate, Leucoraja erinacea.

Proper citation: University of Delaware Skate Genome Project (RRID:SCR_005300) Copy   

•   Source: SciCrunch Registry

http://noble.gs.washington.edu/proj/genomedata/

A format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint. They have also developed utilities to load data into this format. Retrieving data from this format is more than 2900 times faster than a naive approach using wiggle files. A reference implementation in Python and C components is available here under the GNU General Public License. The software has only been tested on Linux and Mac systems.

Proper citation: Genomedata (RRID:SCR_004544) Copy   

•   Source: SciCrunch Registry

http://montana.eagle-i.net/i/0000012b-00be-4e65-df3b-3fdc80000000

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27, 2023. Core for Microarray analysis, Database development, Systems biology analysis, Genome assembly, Pathway data analysis, Expression data analysis, Metagenomics analysis. To maintain equipment and software for bioinformatic research, promote bioinformatics education on the MSU campus, and provide training and support to biologists implementing bioinformatics tools in their research.

Proper citation: Montana State University Bioinformatics Core Facility (RRID:SCR_009937) Copy   

•   Source: SciCrunch Registry

https://github.com/MicrosoftGenomics/FaST-LMM

FaST-LMM (Factored Spectrally Transformed Linear Mixed Models) is a set of tools for efficiently performing genome-wide association studies (GWAS), prediction, and heritability estimation on large data sets.

Proper citation: FaST LMM (RRID:SCR_015506) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ipig/

Standalone software tool for the integration of peptide identifications from mass spectrometry experiments into existing genome browser visualizations.

Proper citation: iPiG (RRID:SCR_016164) Copy   

•   Source: SciCrunch Registry

https://github.com/HMPNK/CSA2.6

Software pipeline for high-throughput chromosome level vertebrate genome assembly. Pipeline, which after contig assembly performs post assembly improvements by ordering assembly and closing gaps, as well as splitting of low supported regions.

Proper citation: Chromosome Scale Assembler (RRID:SCR_017960) Copy   

•   Source: SciCrunch Registry

https://github.com/gatech-genemark/ProtHint

Software pipeline for predicting and scoring hints (in form of introns, start and stop codons) in genome of interest by mapping and spliced aligning predicted genes to database of reference protein sequences.

Proper citation: ProtHint (RRID:SCR_021167) Copy   

•   Source: SciCrunch Registry

http://www.plantcyc.org/

Collaborative project to bring together biochemical pathway databases and research communities focused on plant metabolism. Used to build broad network of plant metabolic pathway databases. Central feature of PMN is PlantCyc, comprehensive plant biochemical pathway database, containing curated information from literature and computational analyses about genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism.

Proper citation: Plant Metabolic Network (RRID:SCR_002888) Copy   

•   Source: SciCrunch Registry

http://www.jgi.doe.gov/

Institute to advance genomics in support of the DOE missions related to clean energy generation and environmental characterization and cleanup. Supported by the DOE Office of Science, the DOE JGI unites the expertise at Lawrence Berkeley National Laboratory, Lawrence Livermore National Laboratory, and the HudsonAlpha Institute for Biotechnology. The facility provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges.

Proper citation: DOE Joint Genome Institute (RRID:SCR_003045) Copy   

•   Source: SciCrunch Registry

http://lab.rockefeller.edu/casanova/HGC

Data set containing a gene-specific connectome file for each human gene and computer programs for ranking lists of genes within a gene-specific connectome, clustering and plotting the genes by the functional genomic alignment (FGA) approach, and generating gene-specific connectomes. The programs were developed and tested on Mac and Linux systems. The external software required for running these programs is open-source and free of charge. The HGC is the set of all biologically plausible routes, distances, and degrees of separation between all pairs of human genes. A gene-specific connectome contains the set of all available human genes sorted on the basis of their predicted biological proximity to the specific gene of interest. The HGC is a powerful approach for human genotype-phenotype high-throughput studies, for which it can be used to rank any list of genes within a gene-specific connectome for an experimentally validated core gene. Functional genomic alignment (FGA) is equivalent to traditional multiple sequence alignment (MSA), except that it clusters genes in trees on the basis of the functional biological distance between them predicted by HGC, rather than on the basis of molecular evolutionary genetic distance. This method is therefore more suitable for disease and phenotypic studies.

Proper citation: Human Gene Connectome (RRID:SCR_002628) Copy   

•   Source: SciCrunch Registry

http://www.ngfn.de/en/start.html

The program of medical genome research is a large-scale biomedical research project which extends the national genome research net (NGFN) and will be funded by the federal ministry of education and research (BMBF) from 2008-2013. Currently the program includes two fields: * Research ** NGFN-Plus: With the aim on combating diseases that are central to health policy, several hundred researchers are systematically investigating the complex molecular interactions of the human body. They are organized in 26 Integrated Genome Research Networks. * Application ** NGFN-Transfer: The rapid transfer of results from medical genome research into medical and industrial application is the aim of the scientists from research institutes and biomedical enterprises that cooperate in eight Innovation Alliances. AREAS OF DISEASE * Cardiovascular disease * Cancer * Neuronal diseases * Infections and Inflammations * Environmental factors

Proper citation: National Genome Research Network (RRID:SCR_006626) Copy   

•   Source: SciCrunch Registry

http://icebox.lbl.gov:8080/ApolloWebDemo/jbrowse/

WebApollo is an extensible web-based sequence annotation editor for community annotation. No software download is required and the annotations are saved to a centralized database with real-time annotation updating. (The edit server mediates annotation changes made by multiple users.) The Web based client uses JBrowse, is fast and highly interactive. WebApollo accesses many types of genomic data including access to public data from UCSC, Ensembl, and GMOD Chado databases. Source code (BSD License) * Client source code: https://github.com/berkeleybop/jbrowse * Annotation editing engine: http://code.google.com/p/apollo-web * Data model and I/O layer: http://code.google.com/p/gbol * Trellis server code: http://code.google.com/p/genomancer

Proper citation: WebApollo: A Web-Based Sequence Annotation Editor for Community Annotation (RRID:SCR_005321) Copy   

•   Source: SciCrunch Registry

https://github.com/Nextomics/NextPolish

Software tool to fix base errors SNV/Indel in genome generated by noisy reads. Used to correct error bases in reference genome.

Proper citation: NextPolish (RRID:SCR_025232) Copy   

•   Source: SciCrunch Registry

https://github.com/BackofenLab/HVSeeker/tree/main

Software tool for distinguishing between bacterial and phage sequences. Consists of two separate models: one analyzing DNA sequences and the other focusing on proteins.

Proper citation: HVSeeker (RRID:SCR_026120) Copy   

•   Source: SciCrunch Registry

http://www.genome.gov/27549169

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2025. 2012 workshop to establish a Central Resource of Data from Genome Sequencing Projects. The workshop addressed the challenges to aggregating and analyzing data sets from genome sequencing studies, such as: * Data sets being generally hard to access. * Data residing in various databases. * Variant and exposure/phenotype data not being comparable across studies. Participants in the workshop discussed options for dealing with these challenges, along with their costs and tradeoffs. Videos and accompanying slides from the workshop are available. Also available as a video playlist on GenomeTV

Proper citation: NHGRI: Establishing a Central Resource of Data from Genome Sequencing Projects (RRID:SCR_003205) Copy   

•   Source: SciCrunch Registry

http://www.gramene.org

Curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species to facilitate the study of cross-species comparisons using information generated from projects supported by public funds. It currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations. The web-based displays for phenotypes include the Genes and Quantitative Trait Loci (QTL) modules. Sequence based relationships are displayed in the Genomes module using the genome browser adapted from Ensembl, in the Maps module using the comparative map viewer (CMap) from GMOD, and in the Proteins module displays. BLAST is used to search for similar sequences. Literature supporting all the above data is organized in the Literature database. In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data. Additionally you can access Gramene through an FTP site.

Proper citation: Gramene (RRID:SCR_002829) Copy   

•   Source: SciCrunch Registry

http://hembase.niddk.nih.gov/

Database designed for web-based examination of the human erythroid transcriptome. The database is organized to provide a cytogenetic band position, a unique name as well as a concise annotation for each entry. Search queries may be performed by name, keyword or cytogenetic location. Search results are linked to primary sequence data and three major human genome browsers for access to information considered current at the time of each search. Hembase provides interested scientists and clinical hematologists with a genome-based approach toward the study of erythroid biology. Red blood cells in the circulation arise from hematopoietic stem cells that proliferate as erythroid progenitors and differentiate into erythroid precursor cells in response to the hormone erythropoietin. Messenger RNA was isolated from those cells and used to generate gene libraries. Sequencing several thousand expressed sequence tags (EST) from those libraries was then performed. Those EST and sequences encoding several hundred additional genes with known expression in erythroid cells are compiled here as a database of human erythroid gene activity. The database is organized and linked according to the location of these sequences within the human genome., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

Proper citation: HemBase (RRID:SCR_002880) Copy   

•   Source: SciCrunch Registry