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http://www.unil.ch/comparativegenometrics/

The Comparative Genometrics website displays for sequenced genomes, three different genometric analyses: the DNA walk and the GC and TA skews during the initial phase. Although primarily focused on prokaryotic chromosomes, the CG website posts genometric information on paradigm plasmids, phages, viruses, and organelles. The genometric analyses are available via phylogenetic tree or alphabetical list. It also offers small genome information, for mitochondria, chloroplasts, viruses, bacteriophages, and plasmids.

Proper citation: Comparative Genometrics (RRID:SCR_012920) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/Projects/D_rerio/

Database of zebrafish genome.

Proper citation: Zebrafish Genome Project (RRID:SCR_013157) Copy   

•   Source: SciCrunch Registry

http://www.treefam.org

A database of phylogenetic trees of animal genes. It aims at developing a curated resource that gives reliable information about ortholog and paralog assignments, and evolutionary history of various gene families. TreeFam defines a gene family as a group of genes that evolved after the speciation of single-metazoan animals. It also tries to include outgroup genes like yeast (S. cerevisiae and S. pombe) and plant (A. thaliana) to reveal these distant members.TreeFam is also an ortholog database. Unlike other pairwise alignment based ones, TreeFam infers orthologs by means of gene trees. It fits a gene tree into the universal species tree and finds historical duplications, speciations and losses events. TreeFam uses this information to evaluate tree building, guide manual curation, and infer complex ortholog and paralog relations.The basic elements of TreeFam are gene families that can be divided into two parts: TreeFam-A and TreeFam-B families. TreeFam-B families are automatically created. They might contain errors given complex phylogenies. TreeFam-A families are manually curated from TreeFam-B ones. Family names and node names are assigned at the same time. The ultimate goal of TreeFam is to present a curated resource for all the families. phylogenetic tree, animal, vertebrate, invertebrate, gene, ortholog, paralog, evolutionary history, gene families, single-metazoan animals, outgroup genes like yeast (S. cerevisiae and S. pombe), plant (A. thaliana), historical duplications, speciations, losses, Human, Genome, comparative genomics

Proper citation: Tree families database (RRID:SCR_013401) Copy   

•   Source: SciCrunch Registry

http://dorina.mdc-berlin.de/rbp_browser/dorina.html

In animals, RNA binding proteins (RBPs) and microRNAs (miRNAs) post-transcriptionally regulate the expression of virtually all genes by binding to RNA. Recent advances in experimental and computational methods facilitate transcriptome-wide mapping of these interactions. It is thought that the combinatorial action of RBPs and miRNAs on target mRNAs form a post-transcriptional regulatory code. We provide a database that supports the quest for deciphering this regulatory code. Within doRiNA, we are systematically curating, storing and integrating binding site data for RBPs and miRNAs. Users are free to take a target (mRNA) or regulator (RBP and/or miRNA) centric view on the data. We have implemented a database framework with short query response times for complex searches (e.g. asking for all targets of a particular combination of regulators). All search results can be browsed, inspected and analyzed in conjunction with a huge selection of other genome-wide data, because our database is directly linked to a local copy of the UCSC genome browser. At the time of writing, doRiNA encompasses RBP data for the human, mouse and worm genomes. For computational miRNA target site predictions, we provide an update of PicTar predictions.

Proper citation: doRiNA (RRID:SCR_013222) Copy   

•   Source: SciCrunch Registry

http://proline.bic.nus.edu.sg/dedb/

Database on Drosophila melanogaster exons presented in a splicing graph form. Data is based on release 3.2 of the Drosophila melanogaster genome annotations available at FlyBase. The gene structure information extracted from the annotations were checked, clustered and transformed into splicing graph. The splicing graph form of the gene constructs were then used for classification of the various types of alternative splicing events. In addition, Pfam domains were mapped onto the gene structure. Users can query the database using the query page using BLAST, FlyBase Gene Name, FlyBase Gene Symbol, Pfam Accession Number and Pfam Identifier. This allows users to determine the Drosophila melanogaster homology of their gene using a BLAST search and to visualize the alternative splicing variants if any. Users can also determine genes containing a particular domain using the Pfam Accession Numbers and Identifiers.

Proper citation: Drosophila melanogaster Exon Database (RRID:SCR_013441) Copy   

•   Source: SciCrunch Registry

http://toxodb.org/toxo/

A genome and functional genomic database for the protozoan parasite Toxoplasma gondii. It incorporates the sequence and annotation of the T. gondii ME49 strain, as well as genome sequences for the GT1, VEG and RH (Chr Ia, Chr Ib) strains. Sequence information is integrated with various other genomic-scale data, including community annotation, ESTs, gene expression and proteomics data. Organisms * Toxoplasma gondii (ME49, RH, GT1, Veg strains) * Neospora caninum * environmental isolate sequences from numerous species Tools * BLAST: Identify Sequence Similarities * Sequence Retrieval: Retrieve Specific Sequences using IDs and coordinates * PubMed and Entrez: View the Latest Toxoplasma, Neospora Pubmed and Entrez Results * Genome Browser: View Sequences and Features in the genome browser * Ancillary Genome Browse: Access Additional info like Probeset data and Toxoplasma Array info

Proper citation: ApiDB ToxoDB (RRID:SCR_013453) Copy   

•   Source: SciCrunch Registry

http://www.echinobase.org/

Database that provide a genomic information and comparative genomics platform on sea urchins and related echinoderms. It provide collection of information to directly support experimental work on these useful research models in cell and developmental biology.

Proper citation: EchinoBase (RRID:SCR_013732) Copy   

•   Source: SciCrunch Registry

http://www.kazusa.or.jp/kaos/

This site has been developed by Kazusa DNA Research Institute for the purpose of offering the science community the analyzed sequence data produced by a multi-national Arabidopsis genome sequencing project coordinated by the Arabidopsis Genome Initiatives (AGI). The aim of this service is to enable users to browse the annotated sequence data produced by all the sequencing teams of AGI through an user-friendly graphic display system and search engines. Gene structures proposed on the annotated sequences as well as those predicted by computer programs are presented and each graphic item has a hyperlink to detailed information of the corresponding area. The nucleotide sequence data deposited in GenBank by AGI was downloaded, re-computer-analyzed at Kazusa and parsed results are displayed graphically.

Proper citation: Kazusa Arabidopsis data opening site (RRID:SCR_013511) Copy   

•   Source: SciCrunch Registry

http://www.informatics.jax.org/genes.shtml

Searchable database of mouse genes, DNA segments, cytogenetic markers and QTLs. MGI provides access to integrated data on mouse genes and genome features, from sequences and genomic maps to gene expression and disease models.

Proper citation: Genes, Genome Features and Maps (RRID:SCR_017524) Copy   

•   Source: SciCrunch Registry

http://www.mqtldb.org/

Data collection of large scale genome wide DNA methylation analysis of 1,000 mother-child pairs at serial time points across life course (ARIES).

Proper citation: mqtldb (RRID:SCR_018002) Copy   

•   Source: SciCrunch Registry

http://promoter.bx.psu.edu/hi-c/

Genome Browser for study of 3D genome organization and gene regulation and data visualization. Used to visualizing chromatin interaction data, browse other omics data such as ChIP-Seq or RNA-Seq for same genomic region, and gain complete view of both regulatory landscape and 3D genome structure for any given gene., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: 3D Genome (RRID:SCR_017525) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/order/catalog/product/00-0210

Scanner for microarray analysis to scan next-generation higher-density arrays, including SNP arrays, tiling arrays for transcription and all-exon arrays for whole-genome analysis.

Proper citation: GeneChip™ Scanner 3000 7G (RRID:SCR_016522) Copy   

•   Source: SciCrunch Registry

http://crispor.tefor.net

Web application that helps design, evaluate and clone guide sequences for the CRISPR/Cas9 system. This sgRNA design tool assists with guide selection in a variety of genomes and pre-calculated results for all human coding exons as a UCSC Genome Browser track.

Proper citation: CRISPOR (RRID:SCR_015935) Copy   

•   Source: SciCrunch Registry

https://reich.hms.harvard.edu/software

Software application that finds skews in ancestry that are potentially associated with disease genes in recently mixed populations like African Americans. It can be downloaded for either UNIX or Linux.

Proper citation: Ancestrymap (RRID:SCR_004353) 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://cell-innovation.nig.ac.jp/maser/Tools/visualization_top_en.html

One stop platform for NGS big data from analysis to visualization. There are about 400 analysis pipelines integrated on Maser. List of all analysis pipelines, including descriptions and approximate execution times, can be found on page for ‘All pipelines’ in the User Guide.. Regist custom genome software registers custom genomes to Genome Explorer (IN: FASTA).

Proper citation: regist custom genome (RRID:SCR_015999) Copy   

•   Source: SciCrunch Registry

https://www.mc.vanderbilt.edu/victr/dcc/projects/acc/index.php/Main_Page

A national consortium formed to develop, disseminate, and apply approaches to research that combine DNA biorepositories with electronic medical record (EMR) systems for large-scale, high-throughput genetic research. The consortium is composed of seven member sites exploring the ability and feasibility of using EMR systems to investigate gene-disease relationships. Themes of bioinformatics, genomic medicine, privacy and community engagement are of particular relevance to eMERGE. The consortium uses data from the EMR clinical systems that represent actual health care events and focuses on ethical issues such as privacy, confidentiality, and interactions with the broader community.

Proper citation: eMERGE Network: electronic Medical Records and Genomics (RRID:SCR_007428) Copy   

•   Source: SciCrunch Registry

http://www.gene-regulation.com/pub/databases.html

In an effort to strongly support the collaborative nature of scientific research, BIOBASE offers academic and non-profit organizations free access to reduced functionality versions of their products. TRANSFAC Professional provides gene regulation analysis solutions, offering the most comprehensive collection of eukaryotic gene regulation data. The professional paid subscription gives customers access to up-to-date data and tools not available in the free version. The public databases currently available for academic and non-profit organizations are: * TRANSFAC: contains data on transcription factors, their experimentally-proven binding sites, and regulated genes. Its broad compilation of binding sites allows the derivation of positional weight matrices. * TRANSPATH: provides data about molecules participating in signal transduction pathways and the reactions they are involved in, resulting in a complex network of interconnected signaling components.TRANSPATH focuses on signaling cascades that change the activities of transcription factors and thus alter the gene expression profile of a given cell. * PathoDB: is a database on pathologically relevant mutated forms of transcription factors and their binding sites. It comprises numerous cases of defective transcription factors or mutated transcription factor binding sites, which are known to cause pathological defects. * S/MARt DB: presents data on scaffold or matrix attached regions (S/MARs) of eukaryotic genomes, as well as about the proteins that bind to them. S/MARs organize the chromatin in the form of functionally independent loop domains gained increasing support. Scaffold or Matrix Attached Regions (S/MARs) are genomic DNA sequences through which the chromatin is tightly attached to the proteinaceous scaffold of the nucleus. * TRANSCompel: is a database on composite regulatory elements affecting gene transcription in eukaryotes. Composite regulatory elements consist of two closely situated binding sites for distinct transcription factors, and provide cross-coupling of different signaling pathways. * PathoSign Public: is a database which collects information about defective cell signaling molecules causing human diseases. While constituting a useful data repository in itself, PathoSign is also aimed at being a foundational part of a platform for modeling human disease processes.

Proper citation: Gene Regulation Databases (RRID:SCR_008033) Copy   

•   Source: SciCrunch Registry

http://cgems.cancer.gov

The project began as a pilot study to identify inherited genetic susceptibility to prostate and breast cancer. CGEMS has developed into a robust research program involving genome-wide association studies (GWASs) for a number of cancers to identify common genetic variants that affect a person''s risk of developing cancer. In collaboration with extramural scientists, NCI''s Division of Cancer Epidemiology and Genetics (DCEG) has carried out genome-wide scans for breast, prostate, pancreatic, and lung cancers, while a GWAS of bladder cancer is currently underway. By making the data available to both intramural and extramural research scientists, as well as those in the private sector through rapid posting, NIH can leverage its resources to ensure that the dramatic advances in genomics are incorporated into rigorous population-based studies. Ultimately, findings from these studies may yield new preventive, diagnostic, and therapeutic interventions for cancer. Sponsors: This resource is supported by the U.S. National Institues Of Health.

Proper citation: CGEMS (RRID:SCR_008445) Copy   

•   Source: SciCrunch Registry

http://cgap.nci.nih.gov/

Project to determine the gene expression profiles of normal, precancer, and cancer cells, whose generated resources are available to the cancer community. Interconnected modules provide access to all CGAP data, bioinformatic analysis tools, and biological resources allowing the user to find in silico answers to biological questions in a fraction of the time it once took in the laboratory. * Genes * Tissues * Pathways * RNAi * Chromosomes * SAGE Genie * Tools

Proper citation: Cancer Genome Anatomy Project (RRID:SCR_003072) Copy   

•   Source: SciCrunch Registry