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http://mitobreak.portugene.com/cgi-bin/Mitobreak_home.cgi

Database with curated datasets of mitochondrial DNA (mtDNA) rearrangements. Users may submit new mtDNA rearrangements.

Proper citation: MitoBreak (RRID:SCR_012949) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ngsep/

Software whose main functionality is the variants detector, which allows to make simultaneous discovery of SNVs, small indels, and CNVs.Accurate variant calling across species and sequencing protocols.Used for analysis of DNA high throughput sequencing data.

Proper citation: NGSEP (RRID:SCR_012827) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/minfi.html

Software tools for analyzing and visualizing Illumina''s 450k array data.

Proper citation: minfi (RRID:SCR_012830) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/affy.html

Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis.

Proper citation: affy (RRID:SCR_012835) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/edgeR/

Bioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication.

Proper citation: edgeR (RRID:SCR_012802) Copy   

•   Source: SciCrunch Registry

http://www.imgt.org/

A high-quality integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrate species, and in the immunoglobulin superfamily (IgSF), MHC superfamily (MhcSF) and related proteins of the immune system (RPI) of vertebrates and invertebrates, serving as the global reference in immunogenetics and immunoinformatics. IMGT provides a common access to sequence, genome and structure Immunogenetics data, based on the concepts of IMGT-ONTOLOGY and on the IMGT Scientific chart rules. IMGT works in close collaboration with EBI (Europe), DDBJ (Japan) and NCBI (USA). IMGT consists of sequence databases, genome database, structure database, and monoclonal antibodies database, Web resources and interactive tools.

Proper citation: IMGT - the international ImMunoGeneTics information system (RRID:SCR_012780) Copy   

•   Source: SciCrunch Registry

http://web.cmb.usc.edu/people/alber/Software/tomominer/

Software platform for large-scale cryo electron subtomogram classification, alignment, and averaging.

Proper citation: TomoMiner (RRID:SCR_015045) Copy   

•   Source: SciCrunch Registry

http://dnatraffic.ibb.waw.pl/

DNAtraffic database is dedicated to be an unique comprehensive and richly annotated database of genome dynamics during the cell life. DNAtraffic contains extensive data on the nomenclature, ontology, structure and function of proteins related to control of the DNA integrity mechanisms such as chromatin remodeling, DNA repair and damage response pathways from eight model organisms commonly used in the DNA-related study: Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Escherichia coli and Arabidopsis thaliana. DNAtraffic contains comprehensive information on diseases related to the assembled human proteins. Database is richly annotated in the systemic information on the nomenclature, chemistry and structure of the DNA damage and drugs targeting nucleic acids and/or proteins involved in the maintenance of genome stability. One of the DNAtraffic database aim is to create the first platform of the combinatorial complexity of DNA metabolism pathway analysis. Database includes illustrations of pathway, damage, protein and drug. Since DNAtraffic is designed to cover a broad spectrum of scientific disciplines it has to be extensively linked to numerous external data sources. Database represents the result of the manual annotation work aimed at making the DNAtraffic database much more useful for a wide range of systems biology applications. DNAtraffic database is freely available and can be queried by the name of DNA network process, DNA damage, protein, disease, and drug.

Proper citation: DNAtraffic (RRID:SCR_008886) Copy   

•   Source: SciCrunch Registry

http://rsat.ulb.ac.be/rsat/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Retrieve-ensembl-seq is included in the software suite regulatory sequence analysis tools (RSAT), allowing instant submission of retrieved sequences to further analysis tools. AVAILABILITY: retrieve-ensembl-seq is integrated in the RSAT suite: http://rsat.ulb.ac.be/rsat. Web site: http://rsat.ulb.ac.be/rsat/retrieve-ensembl-seq_form.cgi. Web services: http://rsat.ulb.ac.be/rsat/web_services/RSATWS.wsdl. Stand-alone distribution: freely available under an academic licence to download from the RSAT web site. The complete manual, a convenient tutorial and demos are available from the RSAT website. Additional help can be found on the RSAT public forum.

Proper citation: Regulatory Sequence Analysis Tools (RRID:SCR_008560) Copy   

•   Source: SciCrunch Registry

http://www.cs.tau.ac.il/~spike/

Database of curated human signaling pathways with an associated interactive software tool for analysis and dynamic visualization of pathways. Individual pathway maps can be viewed and downloaded; the entire database may be browsed, or launched via a map viewer tool that allows dynamic visualization of the database and save networks in XGMML format that can be viewed in all generic XGMML viewers. Map Topics * Cell cycle progress and check points * DNA damage response * Programmed cell death related processes * Stress-activated transcription factors * Mitogen-activated protein kinase pathways * Immune response signaling * HEarSpike: hearing related pathways

Proper citation: SPIKE (RRID:SCR_010466) Copy   

•   Source: SciCrunch Registry

http://www.findbase.org

FINDbase Worldwide is an online repository of information about the frequency of different mutations leading to inherited disorders in various populations around the globe. Frequency data about 32 disorders, 25 genes within 98 populations covering 1226 mutations is now available. 28 curators worldwide contributed to this database containing data from 37 submissions.

Proper citation: FINDbase Worldwide (RRID:SCR_012744) Copy   

•   Source: SciCrunch Registry

http://data-analysis.charite.de/care/

Comprehensive database of cancer relevant proteins and compound interactions supported by experimental knowledge.Knowledgebase for drug-target relationships related to cancer as well as for supporting information or experimental data.

Proper citation: CancerResource (RRID:SCR_011945) Copy   

•   Source: SciCrunch Registry

http://evs.gs.washington.edu/EVS/

The goal of the project is to discover novel genes and mechanisms contributing to heart, lung and blood disorders by pioneering the application of next-generation sequencing of the protein coding regions of the human genome across diverse, richly-phenotyped populations and to share these datasets and findings with the scientific community to extend and enrich the diagnosis, management and treatment of heart, lung and blood disorders. The groups participating and collaborating in the NHLBI GO ESP include: Seattle GO - University of Washington, Seattle, WA Broad GO - Broad Institute of MIT and Harvard, Cambridge, MA WHISP GO - Ohio State University Medical Center, Columbus, OH Lung GO - University of Washington, Seattle, WA WashU GO - Washington University, St. Louis, MO Heart GO - University of Virginia Health System, Charlottesville, VA ChargeS GO - University of Texas Health Sciences Center at Houston

Proper citation: NHLBI Exome Sequencing Project (ESP) (RRID:SCR_012761) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/thornton-srv/databases/MACiE/

MACiE, which stands for Mechanism, Annotation and Classification in Enzymes, is a collaborative project on enzyme reaction mechanisms. MACiE currently contains 223 fully annotated enzyme reaction mechanisms, which comprise 218 EC numbers (161 EC sub-subclasses) and 310 distinct CATH codes. It is a joint effortbetween the Mitchell Group at the Unilever Centre for Molecular Informatics part of the University of Cambridge and the Thornton Group at the European Bioinformatics Institute.

Proper citation: MACiE (RRID:SCR_013296) Copy   

•   Source: SciCrunch Registry

http://www.h-invitational.jp/

H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats) , relation with diseases, gene expression profiling, and molecular evolutionary features , protein-protein interactions (PPIs) and gene families/groups. This database is produced by the Genome Information Integration Project (2005-) based upon the annotation technology established in the H-Invitational Project for annotation of human full-length cDNAs.

Proper citation: H-InvDB (RRID:SCR_013265) Copy   

•   Source: SciCrunch Registry

http://www.fugu-sg.org/

THIS RESOURCE IS NO LONGER IN SERVICE,documented on August 16, 2019. Fugu genome is among the smallest vertebrate genomes and has proved to be a valuable reference genome for identifying genes and other functional elements such as regulatory elements in the human and other vertebrate genomes, and for understanding the structure and evolution of vertebrate genomes. This site presents version 4 of the Fugu genome, released in October 2004 by the International Fugu Genome Consortium. Fugu rubripes has a very compact genome, with less than 15 consisting of dispersed repetitive sequence, which makes it ideal for gene discovery. A draft sequence of the fugu genome was determined by the International Fugu Genome Consortium in 2002 using the ''whole-genome shotgun'' sequencing strategy. Fugu is the second vertebrate genome to be sequenced, the first being the human genome. This webpage presents the annotation made on the fourth assembly by the IMCB team using the Ensembl annotation pipeline. We are continuing with the gap filling work and linking of the scaffolds to obtain super-contigs.

Proper citation: Fugu Genome Project (RRID:SCR_013014) Copy   

•   Source: SciCrunch Registry

http://zope.bioinfo.cnio.es/plan2l/plan2l.html

A web-based online search system that integrates text mining and information extraction techniques to access systematically information useful for analyzing genetic, cellular and molecular aspects of the plant model organism Arabidopsis thaliana. The system facilitates a more efficient retrieval of information relevant to heterogeneous biological topics, from implications in biological relationships at the level of protein interactions and gene regulation, to sub-cellular locations of gene products and associations to cellular and developmental processes, i.e. cell cycle, flowering, root, leaf and seed development. Beyond single entities, also predefined pairs of entities can be provided as queries for which literature-derived relations together with textual evidences are returned.

Proper citation: PLAN2L (RRID:SCR_013346) Copy   

•   Source: SciCrunch Registry

http://www.deathdomain.org/

A manually curated database of protein-protein interactions for Death Domain Superfamily. The Death Domain Database provides a detailed summary of PPI data, which fits into 3 categories: interaction, characterization, and functional role. Users can find in-depth information specified in the literature on relevant analytical methods, structural information. The DD superfamily currently comprises four subfamilies: * Death domain (DD) subfamily * Death effector domain (DED) subfamily * Caspase recruitment domain (CARD) subfamily * Pyrin domain (PYD) subfamily

Proper citation: Death Domain database (RRID:SCR_013231) Copy   

•   Source: SciCrunch Registry

http://unicarb-db.biomedicine.gu.se

An experimental glycomic MS database initially created to meet the in-house need to store structural and MS-glycomic data. Users can search by taxonomy and tissue, mass and composition, and MS/MS.

Proper citation: UniCarb-DB (RRID:SCR_014407) 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