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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
http://www.atgc-montpellier.fr/mpscan/
Web tool for index free mapping of multiple short reads on a genome.
Proper citation: MPscan (RRID:SCR_000587) Copy
A C++ application designed for compression of genome collections from the same species.
Proper citation: GDC (RRID:SCR_001007) Copy
International collaborative research project and database of annotated mammalian genome. Used to improve estimates of total number of genes and their alternative transcript isoforms in both human and mouse. Consortium to assign functional annotations to full length cDNAs that were collected during Mouse Encyclopedia Project at RIKEN.
Proper citation: Functional Annotation of the Mammalian Genome (RRID:SCR_000788) Copy
Laboratory portal of the University of Sao Paulo Molecular Genetics and Bioinformatic Laboratory.
Proper citation: USP Molecular Genetics and Bioinformatics Laboratory (RRID:SCR_000605) Copy
https://github.com/Ensembl/WiggleTools
A multithreaded software library that computes statistics on large numbers of datasets, generating statistical summaries within minutes with limited memory requirements, whether on the whole genome or on selected regions.
Proper citation: WiggleTools (RRID:SCR_001170) Copy
http://www.bioconductor.org/packages/2.10/bioc/html/R453Plus1Toolbox.html
R software toolbox of functions for the analysis of data generated by Roche's 454 sequencing platform. Additional functions are included for quality assurance, annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. A pipeline for the detection of structural variants is provided.
Proper citation: R453Plus1Toolbox (RRID:SCR_001105) Copy
http://www.morpholinodatabase.org/
Central database to house data on morpholino screens currently containing over 700 morpholinos including control and multiple morpholinos against the same target. A publicly accessible sequence-based search opens this database for morpholinos against a particular target for the zebrafish community. Morpholino Screens: They set out to identify all cotranslationally translocated genes in the zebrafish genome (Secretome/CTT-ome). Morpholinos were designed against putative secreted/CTT targets and injected into 1-4 cell stage zebrafish embryos. The embryos were observed over a 5 day period for defects in several different systems. The first screen examined 184 gene targets of which 26 demonstrated defects of interest (Pickart et al. 2006). A collaboration with the Verfaillie laboratory examined the knockdown of targets identified in a comparative microarray analysis of hematopoietic stem cells demonstrating how microarray and morpholino technologies can be used in conjunction to enrich for defects in specific developmental processes. Currently, many collaborations are underway to identify genes involved in morphological, kidney, skin, eye, pigment, vascular and hematopoietic development, lipid metabolism and more. The screen types referred to in the search functions are the specific areas of development that were examined during the various screens, which include behavior, general morphology, pigmentation, toxicity, Pax2 expression, and development of the craniofacial structures, eyes, kidneys, pituitary, and skin. Only data pertaining to specific tests performed are presented. Due to the complexity of this international collaboration and time constraints, not all morpholinos were subjected to all screen types. They are currently expanding public access to the database. In the future we will provide: * Mortality curves and dose range for each morpholino * Preliminary data regarding the effectiveness of each morpholino * Expanded annotation for each morpholino * External linkage of our morpholino sequences to ZFIN and Ensembl. To submit morpholino-knockdown results to MODB please contact the administrator for a user name and password.
Proper citation: Morpholino Database (RRID:SCR_001378) Copy
http://sourceforge.net/projects/autoassemblyd/
Software which performs local and remote genome assembly by several assemblers based on an XML Template which can replace the large command lines required by most assemblers.
Proper citation: AutoAssemblyD (RRID:SCR_001087) Copy
http://www.genome.jp/kegg/expression/
Database for mapping gene expression profiles to pathways and genomes. Repository of microarray gene expression profile data for Synechocystis PCC6803 (syn), Bacillus subtilis (bsu), Escherichia coli W3110 (ecj), Anabaena PCC7120 (ana), and other species contributed by the Japanese research community.
Proper citation: Kyoto Encyclopedia of Genes and Genomes Expression Database (RRID:SCR_001120) Copy
Data and tools for studying the function of DNA sequences, with an emphasis on those involved in the production of hemoglobin. It includes information about naturally-occurring human hemoglobin mutations and their effects, experimental data related to the regulation of the beta-like globin gene cluster, and software tools for comparing sequences with one another to discover regions that are likely to play significant roles.
Proper citation: Globin Gene Server (RRID:SCR_001480) Copy
Software resource for multiple whole genome alignment. It uses Nucmer, a custom graph-based segmentation procedure, for pairwise alignment, and the Seqan:TCoffee's multiple alignment strategy.
Proper citation: Mugsy (RRID:SCR_001414) Copy
Public database that stores areas of genome that differ between individual genomes (variants) and, where available, associated disease and phenotype information. Different types of variants for several species: single nucleotide polymorphisms (SNPs), short nucleotide insertions and/or deletions, and longer variants classified as structural variants (including CNVs). Effects of variants on the Ensembl transcripts and regulatory features for each species are predicted. You can run same analysis on your own data using Variant Effect Predictor. These data are integrated with other data sources in Ensembl, and can be accessed using the API or website. For several different species in Ensembl, they import variation data (SNPs, CNVs, allele frequencies, genotypes, etc) from a variety of sources (e.g. dbSNP). Imported variants and alleles are subjected to quality control process to flag suspect data. In human, they calculate linkage disequilibrium for each variant, by population.
Proper citation: Ensembl Variation (RRID:SCR_001630) Copy
Web application to search nucleotide databases using a nucleotide query. Algorithms: blastn, megablast, discontiguous megablast.
Proper citation: BLASTN (RRID:SCR_001598) Copy
Web resource that provides data and tools for exploring genomic organization of highly conserved noncoding elements (HCNEs) for multiple genomes. It includes a genome browser that shows HCNE locations and features novel HCNE density plots as a powerful tool to discover developmental regulatory genes and distinguish their regulatory elements and domains. They identify HCNEs as non-exonic regions of high similarity between genome sequences from distantly related organisms, such as human and fish, and provide tools for studying the distribution of HCNEs along chromosomes. Major peaks of HCNE density along chromosomes most often coincide with developmental regulatory genes. Their aim with this site is to aid discovery of developmental regulatory genes, their regulatory domains and their fundamental regulatory elements.
Proper citation: Ancora (RRID:SCR_001623) Copy
Website for analyzing microarray data. Software toolbox for storing, analyzing and integrating microarray data and related genotype and phenotype data. The site is particularly suited for combining QTL and microarray data to search for candidate genes contributing to complex traits. In addition, the site allows, if desired by the investigators, sharing of the data. Investigators can conduct in-silico microarray experiments using their own and/or shared data. There are five major sections of the site: Genome/Transcriptome Data Browser, Microarray Analysis Tools, Gene List Analysis Tools, QTL Tools, and Downloads. The genome/transcriptome data browser combines a genome browser with all the microarray, RNA-Seq, and Genomic Sequencing data. This provides an effective platform to view all of this data side by side. Source code is available on GitHub.
Proper citation: PhenoGen Informatics (RRID:SCR_001613) Copy
http://www.norcomm.org/index.htm
Large-scale research initiative focused on developing and distributing a library of mouse embryonic stem (ES) cell lines carrying single gene trapped or targeted mutations across the mouse genome. NorCOMM's large and growing archive of ES cells is publicly available on a cost-recovery basis from the Canadian Mouse Mutant Repository. As an international public resource, access to clones is unrestricted and nonexclusive. Through NorCOMM's affiliation with the Canadian Mouse Consortium (CMC), NorCOMM also provides clients with a single point of access to regional mouse derivation, phenotyping, genetic and archiving services across Canada. These value-added services can help your company harness NorCOMM's resources for drug discovery, target discovery and preclinical validation.
Proper citation: North American Conditional Mouse Mutagenesis Project (RRID:SCR_001614) Copy
https://www.hgsc.bcm.edu/content/sea-urchin-genome-project
Provides informationa about Genome of California Purple Sea Urchin, one species (Strongylocentrotus purpuratus) of which has been sequenced and annotated by Sea Urchin Genome Sequencing Consortium led by HGSC. Reports sequence and analysis of genome of sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology.
Proper citation: Sea Urchin Genome Project (RRID:SCR_001735) Copy
http://www.animalgenome.org/cgi-bin/QTLdb/index
Database of trait mapping data, i.e. QTL (phenotype / expression, eQTL), candidate gene and association data (GWAS) and copy number variations (CNV) mapped to livestock animal genomes, to facilitate locating and comparing discoveries within and between species. New data and database tools are continually developed to align various trait mapping data to map-based genome features, such as annotated genes. QTLdb is open to house QTL/association date from other animal species where feasible. Most scientific journals require that any original QTL/association data be deposited into public databases before paper may be accepted for publication. User curator accounts are provided for direct data deposit. Users can download QTLdb data from each species or individual chromosome.
Proper citation: Animal QTLdb (RRID:SCR_001748) Copy
http://www.sanbi.ac.za/resources/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. The South African National Bioinformatics Institute delivers biomedical discovery appropriate to both international and African context. Researchers at SANBI perform the highest level of research and provide excellence in education. Research at SANBI has set well recognized milestones in the field of computational biology. The tools and techniques used have not only been developed but also implemented across heterogeneous domains of advanced research. Local and international efforts have driven our discoveries. Until recently, the core of SANBIs research has focused upon gene expression biology. Methods developed and applied at SANBI revolve around a greater understanding of the underlying causes of diseases. SANBI approaches the problem by comparison of genes, genomes and transcriptomes. It uses computational gene expression biology to create novel biological insights and to provide biomarkers for experimental validation. It also performs analysis of human genome variation, transcriptional diversity on both the expression and splicing level and the unravelling of transcriptional regulatory networks. Resources - Hinv, STACKdb, Malaria resources and Trypanosome databases are available for on-line seaching. - SANBI offers WCD, STACKdb, stackPACK and eVOC and the eVOKE viewer as tools that can be downloaded. Sponsors: SANBI receives funding and support from a range of organisations in South Africa and Internationally. Organisations currently supporting SANBI include: South Africa * South African Medical Research Council * South African AIDS Vaccine Initiative * National Bioinformatics Network * National Research Foundation * Claude Leon Foundation * International Business Machines Inc. Europe * European Unions 6th Framework Programme * World Health Organization USA * US National Institutes of Health * Fogarty International Centre * Ludwig Institute for Cancer Research
Proper citation: South African National Bioinformatics Institute: Resources (RRID:SCR_001867) Copy
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