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http://germsage.nichd.nih.gov

Collection of male germ cell transcriptiome information derived from Serial Analysis of Gene Expression (SAGE). It includes the three key germ cell stages in spermatogenesis, including mouse type A spermatogonia (Spga), pachytene spermatocytes (Spcy), and round spermatids (Sptd). A total of 452,095 SAGE tags are represented in all the libraries and is by far the most comprehensive resource available. Users can choose a global view of germ cell transcriptome data in the UCSC Genome browser. They can also search genes or specify searching criteria based on tag sequence, chromosomal location or tag counts.

Proper citation: GermSAGE (RRID:SCR_007689) Copy   

•   Source: SciCrunch Registry

http://mirgator.kobic.re.kr/

Database of compiled, public, deep sequencing miRNA data and several novel tools to facilitate exploration of massive data. The miR-seq browser supports users to examine short read alignment with the secondary structure and read count information available in concurrent windows. Features such as sequence editing, sorting, ordering, import and export of user data are of great utility for studying iso-miRs, miRNA editing and modifications. miRNA����??target relation is essential for understanding miRNA function. Coexpression analysis of miRNA and target mRNAs, based on miRNA-seq and RNA-seq data from the same sample, is visualized in the heat-map and network views where users can investigate the inverse correlation of gene expression and target relations, compiled from various databases of predicted and validated targets.

Proper citation: miRGator (RRID:SCR_007793) Copy   

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http://systers.molgen.mpg.de/

SYSTERS is a database of protein sequences grouped into homologous families and superfamilies. The SYSTERS project aims to provide a meaningful partitioning of the whole protein sequence space by a fully automatic procedure. A refined two-step algorithm assigns each protein to a family and a superfamily. The sequence data underlying SYSTERS release 4 now comprise several protein sequence databases derived from completely sequenced genomes (ENSEMBL, TAIR, SGD and GeneDB), in addition to the comprehensive Swiss-Prot/TrEMBL databases. To augment the automatically derived results, information from external databases like Pfam and Gene Ontology are added to the web server. Furthermore, users can retrieve pre-processed analyses of families like multiple alignments and phylogenetic trees. New query options comprise a batch retrieval tool for functional inference about families based on automatic keyword extraction from sequence annotations. A new access point, PhyloMatrix, allows the retrieval of phylogenetic profiles of SYSTERS families across organisms with completely sequenced genomes. Gene, Human, Vertebrate, Genome, Human ORFs

Proper citation: SYSTERS (RRID:SCR_007955) Copy   

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http://supfam.org/SUPERFAMILY/

SUPERFAMILY is a database of structural and functional protein annotations for all completely sequenced organisms. The SUPERFAMILY annotation is based on a collection of hidden Markov models, which represent structural protein domains at the SCOP superfamily level. A superfamily groups together domains which have an evolutionary relationship. The annotation is produced by scanning protein sequences from over 1,700 completely sequenced genomes against the hidden Markov models.

Proper citation: SUPERFAMILY (RRID:SCR_007952) Copy   

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http://mips.gsf.de/simap/

It provides a database based on a pre-computed similarity matrix covering the similarity space formed by >4 million amino acid sequences from public databases and completely sequenced genomes. The database is capable of handling very large datasets and is updated incrementally. For sequence similarity searches and pairwise alignments, we implemented a grid-enabled software system, which is based on FASTA heuristics and the Smith Waterman algorithm. SimpleSIMAP and AdvancedSIMAP retrieve homologs for given protein sequences that need to be contained in the SIMAP database. While SimpleSIMAP provides only selected parameters and preconfigured search spaces, the AdvancedSIMAP allows the user to specify search space, filtering and sorting parameters in a flexible manner. Both types of queries result in lists of homologs that are linked in turn to their homologs. So the web interfaces allow users to explore quickly and interactively the protein world by homology. Sponsors: SIMAP is supported by the Department of Genome Oriented Bioinformatics of the Technische Universitt Mnchen and the Institute for Bioinformatics of the GSF-National Research Center for Environment and Health.

Proper citation: SIMAP (RRID:SCR_007927) Copy   

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http://mrna.otago.ac.nz/

Database that provides access to mRNA sequences and associated regulatory elements that were processed from Genbank. These mRNA sequences include complete genomes, which are divided into 5-prime UTRs, 3-prime UTRs, initiation sequences, termination regions and full CDS sequences. This data can be searched for a range of properties including specific mRNA sequences, mRNA motifs, codon usage, RSCU values, information content, etc.

Proper citation: Transterm (RRID:SCR_008244) Copy   

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http://www.primervfx.com/#welcome

PrimerParadise is an online PCR primer database for genomics studies. The database contains predesigned PCR primers for amplification of exons, genes and SNPs of almost all sequenced genomes. Primers can be used for genome-wide projects (resequencing, mutation analysis, SNP detection etc). The primers for eukaryotic genomes have been tested with e-PCR to make sure that no alternative products will be generated. Also, all eukaryotic primers have been filtered to exclude primers that bind excessively throughout the genome. Genes are amplified as amplicons. Amplicons are defined as only one genes exons containing maximaly 3000 bp long dna segments. If gene is longer than 3000 bp then it is split into the segments at length 3000 bp. So for example gene at length 5000 bp is split into two segment and for both segments there were designed a separate primerpair. If genes exons length is over 3000 bp then it is split into amplicons as well. Every SNP has one primerpair. In addition of considering repetitive sequences and mono-dinucleotide repeats, we avoid designing primers to genome regions which contain other SNPs. -There are two ways to search for primers: you can use features IDs ( for SNP primers Reference ID, for gene/exon primers different IDs (Ensembl gene IDs, HUGO IDs for human genes, LocusLink IDs, RefSeq IDs, MIM IDs, NCBI gene names, SWISSPROT IDs for bacterial genes, VEGA gene IDs for human and mouse, Sanger S.pombe systematic gene names and common gene names, S.cerevisiae GeneBanks Locus, AccNo, GI IDs and common gene names) -you can use genome regions (chromosome coordinates, chromosome bands if exists) -Currently we provide 3 primers collections: proPCR for prokaryotic organisms genes primers -euPCR for eukaryotic organisms genes/exons primers -snpPCR for eukaryotic organisms SNP primers Sponsors: PrimerStudio is funded by the University of Tartu.

Proper citation: PrimerStudio (RRID:SCR_008232) Copy   

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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   

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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.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.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://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

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

http://www.stsiweb.org/SWGR/

Whole genome sequencing data for 454 unrelated Scripps Wellderly Study participants with European ancestry from a project that is studying the genetic architecture of exceptional healthspan from a cohort comprised of more than 1300 healthy individuals over the age of 80 years. SWGR_v1.0 includes chromosome-specific VCF4.1 bgzipped and tabix indexed files. Annotations for each variant can be found at Scripps Genome ADVISER (SG-ADVISER, http://genomics.scripps.edu/) Additional data releases are expected.

Proper citation: Scripps Wellderly Genome Reference (RRID:SCR_010250) Copy   

•   Source: SciCrunch Registry

https://jmorp.megabank.tohoku.ac.jp/

Japanese multi omics reference panel. Provides multidimensional approach to diversity of Japanese population. Public database for plasma metabolome and proteome analyses. Updated to metabolome, genome, transcriptome, metagenome, number of samples, analysis methods of each dataset, expanding links between each layer and links between hierarchies.

Proper citation: jMORP (RRID:SCR_024755) 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

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

https://gemini.readthedocs.io/en/latest/

Framework for exploring genetic variation in the context of the genome annotations available for the human genome. Users can load a VCF file into a database and each variant is automatically annotated by comparing it to several genome annotations from source such as ENCODE tracks, UCSC tracks, OMIM, dbSNP, KEGG, and HPRD.

Proper citation: GEMINI (RRID:SCR_014819) Copy   

•   Source: SciCrunch Registry

http://www.dnaform.jp/products/cage_e.html

Expression profiling and promoter identification software tool for transcriptional network analysis and transcriptome characterization. DeepCAGE, the combination of next-generation sequencing with next generation expression profiling provides unsurpassed solutions for expression profiling and genome annotation. CAGE will be the experimental approach at need to link gene expression and control regions in the genome. With the availability of next-generation sequencing methods, DNAFORM now offers DeepCAGE services. DeepCAGE libraries are prepared for direct analysis by an Illumina/Solexa Sequencer. One sequencing run using one channel on an Illumina/Solexa Sequencer can yield in over 4,000,000 reads per sample. CAGE is based on our full-length cDNA library technology, where an adaptor is ligated to the 5''''-end of full-length cDNAs, which introduces a recognition site for a Class IIs restriction endonuclease adjacent to the 5''''-end of the cDNA. The Class IIs restriction endonuclease, here MmeI, allows for the cloning of short tags as derived from the 5''''-end of transcripts into concatemers for high-throughput sequencing. CAGE tags are further characterized by mapping to genomic sequences, which enables the identification of transcriptional start sites. As such CAGE can contribute to projects in Gene Discovery, Gene Expression, and Promoter Identification. After the genome sequencing projects have provided us with the genetic blueprints for many organisms, new questions have to be answered on how to correlate the observed genotypes with related phenotypes, and how to understand the regulation of genetic information in time and space. The dynamics of living systems and the functional behavior of cells in multicellular organisms has thus become the subject of the emerging field of system biology. Integration of experimental approaches and computer aided theories on a system level will be the fundamental principle to drive systems biology in order to understand the principles behind complex regulatory networks, which will be an ambitious goal requiring new approaches in life sciences. For ordering and additional information, please contact us under contact_at_dnaform.jp

Proper citation: CAGE (RRID:SCR_007574) Copy   

•   Source: SciCrunch Registry