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http://bioinfo.mbi.ucla.edu/ASAP/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on 8/12/13. Database to access and mine alternative splicing information coming from genomics and proteomics based on genome-wide analyses of alternative splicing in human (30 793 alternative splice relationships found) from detailed alignment of expressed sequences onto the genomic sequence. ASAP provides precise gene exon-intron structure, alternative splicing, tissue specificity of alternative splice forms, and protein isoform sequences resulting from alternative splicing. They developed an automated method for discovering human tissue-specific regulation of alternative splicing through a genome-wide analysis of expressed sequence tags (ESTs), which involves classifying human EST libraries according to tissue categories and Bayesian statistical analysis. They use the UniGene clusters of human Expressed Sequence Tags (ESTs) to identify splices. The UniGene EST's are clustered so that a single cluster roughly corresponds to a gene (or at least a part of a gene). A single EST represents a portion of a processed (already spliced) mRNA. A given cluster contains many ESTs, each representing an outcome of a series of splicing events. The ESTs in UniGene contain the different mRNA isoforms transcribed from an alternatively spliced gene. They are not predicting alternative splicing, but locating it based on EST analysis. The discovered splices are further analyzed to determine alternative splicing events. They have identified 6201 alternative splice relationships in human genes, through a genome-wide analysis of expressed sequence tags (ESTs). Starting with 2.1 million human mRNA and EST sequences, they mapped expressed sequences onto the draft human genome sequence and only accepted splices that obeyed the standard splice site consensus. After constructing a tissue list of 46 human tissues with 2 million human ESTs, they generated a database of novel human alternative splices that is four times larger than our previous report, and used Bayesian statistics to compare the relative abundance of every pair of alternative splices in these tissues. Using several statistical criteria for tissue specificity, they have identified 667 tissue-specific alternative splicing relationships and analyzed their distribution in human tissues. They have validated our results by comparison with independent studies. This genome-wide analysis of tissue specificity of alternative splicing will provide a useful resource to study the tissue-specific functions of transcripts and the association of tissue-specific variants with human diseases.

Proper citation: ASAP: the Alternative Splicing Annotation Project (RRID:SCR_003415) Copy   

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http://dire.dcode.org

Web server based on the Enhancer Identification (EI) method, to determine the chromosomal location and functional characteristics of distant regulatory elements (REs) in higher eukaryotic genomes. The server uses gene co-expression data, comparative genomics, and combinatorics of transcription factor binding sites (TFBSs) to find TFBS-association signatures that can be used for discriminating specific regulatory functions. DiRE's unique feature is the detection of REs outside of proximal promoter regions, as it takes advantage of the full gene locus to conduct the search. DiRE can predict common REs for any set of input genes for which the user has prior knowledge of co-expression, co-function, or other biologically meaningful grouping. The server predicts function-specific REs consisting of clusters of specifically-associated TFBSs, and it also scores the association of individual TFs with the biological function shared by the group of input genes. Its integration with the Array2BIO server allows users to start their analysis with raw microarray expression data.

Proper citation: Distant Regulatory Elements (RRID:SCR_003058) Copy   

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http://www.mitomap.org/

Database of polymorphisms and mutations of the human mitochondrial DNA. It reports published and unpublished data on human mitochondrial DNA variation. All data is curated by hand. If you would like to submit published articles to be included in mitomap, please send them the citation and a pdf.

Proper citation: MITOMAP - A human mitochondrial genome database (RRID:SCR_002996) Copy   

•   Source: SciCrunch Registry

http://www.flytf.org/

A database of genomic and protein data for Drosophila site-specific transcription factors.

Proper citation: FlyTF.org (RRID:SCR_004123) Copy   

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http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=7165

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. A database for the Anopheles gambiae str. PEST genome that was sequenced using a whole genome shotgun approach. The database aims to contribute to the understanding of mosquito genome structure and organization and will assist the development of malaria control strategies and improved anti-malarial drugs and vaccines. Sequences were generated and assembled into contigs for submission to GenBank.

Proper citation: Anopheles gambiae (African malaria mosquito) genome view (RRID:SCR_004402) 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

http://www.labspaces.net/DNA

Hi. I''m genegeek (aka Catherine Anderson). I realized during my PostDoc that I preferred learning and explaining new results to doing science so I started a non-traditional career of teaching and outreach. I''ll be using this space to explore public perception of genetics and other cool molecular biology stuff. I hope to add to the great discussions re: new science discoveries and general understanding of genetics. I''ve been running an outreach program and enjoy talking to non-experts about their opinions and understanding. I hope my enthusiasm for the topics can come through the screen. My posts are presented as opinion and commentary and do not represent the views of LabSpaces Productions, LLC, my employer, or my educational institution.

Proper citation: Daring Nucleic Adventures - genegeek (RRID:SCR_005215) Copy   

•   Source: SciCrunch Registry

http://www.knockoutmouse.org/

Database of the international consortium working together to mutate all protein-coding genes in the mouse using a combination of gene trapping and gene targeting in C57BL/6 mouse embryonic stem (ES) cells. Detailed information on targeted genes is available. The IKMC includes the following programs: * Knockout Mouse Project (KOMP) (USA) ** CSD, a collaborative team at the Children''''s Hospital Oakland Research Institute (CHORI), the Wellcome Trust Sanger Institute and the University of California at Davis School of Veterinary Medicine , led by Pieter deJong, Ph.D., CHORI, along with K. C. Kent Lloyd, D.V.M., Ph.D., UC Davis; and Allan Bradley, Ph.D. FRS, and William Skarnes, Ph.D., at the Wellcome Trust Sanger Institute. ** Regeneron, a team at the VelociGene division of Regeneron Pharmaceuticals, Inc., led by David Valenzuela, Ph.D. and George D. Yancopoulos, M.D., Ph.D. * European Conditional Mouse Mutagenesis Program (EUCOMM) (Europe) * North American Conditional Mouse Mutagenesis Project (NorCOMM) (Canada) * Texas A&M Institute for Genomic Medicine (TIGM) (USA) Products (vectors, mice, ES cell lines) may be ordered from the above programs.

Proper citation: International Knockout Mouse Consortium (RRID:SCR_005574) Copy   

•   Source: SciCrunch Registry

http://swissregulon.unibas.ch/fcgi/sr/swissregulon

A database of genome-wide annotations of regulatory sites. The predictions are based on Bayesian probabilistic analysis of a combination of input information including: * Experimentally determined binding sites reported in the literature. * Known sequence-specificities of transcription factors. * ChIP-chip and ChIP-seq data. * Alignments of orthologous non-coding regions. Predictions were made using the PhyloGibbs, MotEvo, IRUS and ISMARA algorithms developed in their group, depending on the data available for each organism. Annotations can be viewed in a Gbrowse genome browser and can also be downloaded in flat file format.

Proper citation: SwissRegulon (RRID:SCR_005333) Copy   

•   Source: SciCrunch Registry

http://transpogene.tau.ac.il/

A publicly available database of Transposed elements (TEs) which are located within protein-coding genes of 7 organisms: human, mouse, chicken, zebrafish, fruilt fly, nematode and sea squirt. Using TranspoGene the user can learn about the many aspects of the effect these TEs have on their hosting genes, such as: exonization events (including alternative splicing-related data), insertion of TEs into introns, exons, and promoters, specific location of the TE over the gene, evolutionary divergence of the TE from its consensus sequence and involvement in diseases. TranspoGene database is quickly searchable through its website, enables many kinds of searches and is available for download. TranspoGene contains information regarding specific type and family of the TEs, genomic and mRNA location, sequence, supporting transcript accession and alignment to the TE consensus sequence. The database also contains host gene specific data: gene name, genomic location, Swiss-Prot and RefSeq accessions, diseases associated with the gene and splicing pattern. The TranspoGene and microTranspoGene databases can be used by researchers interested in the effect of TE insertion on the eukaryotic transcriptome.

Proper citation: TranspoGene (RRID:SCR_005634) Copy   

•   Source: SciCrunch Registry

http://tabit.ucsd.edu/sdec/

A next-generation web-based application that aims to provide an integrated solution for both visualization and analysis of deep-sequencing data, along with simple access to public datasets.

Proper citation: Systems Transcriptional Activity Reconstruction (RRID:SCR_005622) 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

http://cell-innovation.nig.ac.jp/maser/AllPipelines/P000001138_en.html

Software pipeline that visualizes mapping results (in BAM format) on Genome Explorer.

Proper citation: loadBAM2ge_db (RRID:SCR_015951) Copy   

•   Source: SciCrunch Registry

https://blobtoolkit.genomehubs.org/blobtools2/

Software suite for identifying and isolating non-target data in draft and publicly available genome assemblies. Used to process assembly, read and analysis files for fully reproducible interactive exploration in browser-based Viewer. Used for interactive quality assessment of genome assemblies .BlobTools2 is reimplementation of BlobTools, written in Python 3 with fully modular design to make creating new datasets and adding additional analysis types easier.

Proper citation: BlobTools2 (RRID:SCR_023351) 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

http://gmdd.shgmo.org/Computational-Biology/GRS/

A compression tool for efficient storage of Genome Re-Sequencing data. GRS processes genome sequence data without use of reference SNPs and other variants. It can also automatically rebuild the individual genome sequence data using the reference genome sequence.

Proper citation: GRS (RRID:SCR_001008) Copy   

•   Source: SciCrunch Registry

http://ntap.cbi.pku.edu.cn/usage.php

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for tiling array data analysis to survey the genome-wide binding sites of transcription factor HY5 in Arabidopsis and the genome-wide histone modifications/DNA methylation level in rice. It was developed in the process of generating NimbleGen analysis. Written in R and Perl.

Proper citation: NTAP (RRID:SCR_001488) Copy   

•   Source: SciCrunch Registry

http://www.patricbrc.org/portal/portal/patric/Home

A Bioinformatics Resource Center bacterial bioinformatics database and analysis resource that provides researchers with an online resource that stores and integrates a variety of data types (e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data) and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes, currently more than 10 000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. The PATRIC project includes three primary collaborators: the University of Chicago, the University of Manchester, and New City Media. The University of Chicago is providing genome annotations and a PATRIC end-user genome annotation service using their Rapid Annotation using Subsystem Technology (RAST) system. The National Centre for Text Mining (NaCTeM) at the University of Manchester is providing literature-based text mining capability and service. New City Media is providing assistance in website interface development. An FTP server and download tool are available.

Proper citation: Pathosystems Resource Integration Center (RRID:SCR_004154) Copy   

•   Source: SciCrunch Registry

http://www.GeneWeaver.org

Freely accessible phenotype-centered database with integrated analysis and visualization tools. It combines diverse data sets from multiple species and experiment types, and allows data sharing across collaborative groups or to public users. It was conceived of as a tool for the integration of biological functions based on the molecular processes that subserved them. From these data, an empirically derived ontology may one day be inferred. Users have found the system valuable for a wide range of applications in the arena of functional genomic data integration.

Proper citation: Gene Weaver (RRID:SCR_003009) Copy   

•   Source: SciCrunch Registry