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http://mips.gsf.de/genre/proj/ustilago/

The MIPS Ustilago maydis Genome Database aims to present information on the molecular structure and functional network of the entirely sequenced, filamentous fungus Ustilago maydis. The underlying sequence is the initial release of the high quality draft sequence of the Broad Institute. The goal of the MIPS database is to provide a comprehensive genome database in the Genome Research Environment in parallel with other fungal genomes to enable in depth fungal comparative analysis. The specific aims are to: 1. Generate and assemble Whole Genome Shotgun sequence reads yielding 10X coverage of the U. maydis genome 2. Integrate the genomic sequence assembly with physical maps generated by Bayer CropScience 3. Perform automated annotation of the sequence assembly 4. Align the strain 521 assembly with the FB1 assembly provided by Exelixis 5. Release the sequence assembly and results of our annotation and analysis to public Ustilago maydis is a basidiomycete fungal pathogen of maize and teosinte. The genome size is approximately 20 Mb. The fungus induces tumors on host plants and forms masses of diploid teliospores. These spores germinate and form haploid meiotic products that can be propagated in culture as yeast-like cells. Haploid strains of opposite mating type fuse and form a filamentous, dikaryotic cell type that invades plant tissue to reinitiate infection. Ustilago maydis is an important model system for studying pathogen-host interactions and has been studied for more than 100 years by plant pathologists. Molecular genetic research with U. maydis focuses on recombination, the role of mating in pathogenesis, and signaling pathways that influence virulence. Recently, the fungus has emerged as an excellent experimental model for the molecular genetic analysis of phytopathogenesis, particularly in the characterization of infection-specific morphogenesis in response to signals from host plants. Ustilago maydis also serves as an important model for other basidiomycete plant pathogens that are more difficult to work with in the laboratory, such as the rust and bunt fungi. Genomic sequence of U. maydis will also be valuable for comparative analysis of other fungal genomes, especially with respect to understanding the host range of fungal phytopathogens. The analysis of U. maydis would provide a framework for studying the hundreds of other Ustilago species that attack important crops, such as barley, wheat, sorghum, and sugarcane. Comparisons would also be possible with other basidiomycete fungi, such as the important human pathogen C. neoformans. Commercially, U. maydis is an excellent model for the discovery of antifungal drugs. In addition, maize tumors caused by U. maydis are prized in Hispanic cuisine and there is interest in improving commercial production. The complete putative gene set of the Broad Institute''s second release is loaded into the database and in addition all deviating putative genes from a putative gene set produced by MIPS with different gene prediction parameters are also loaded. The complete dataset will then be analysed, gene predictions will be manually corrected due to combined information derived from different gene prediction algorithms and, more important, protein and EST comparisons. Gene prediction will be restricted to ORFs larger than 50 codons; smaller ORFs will be included only if similarities to other proteins or EST matches confirm their existence or if a coding region was postulated by all prediction programs used. The resulting proteins will be annotated. They will be classified according to the MIPS classification catalogue receiving appropriate descriptions. All proteins with a known, characterized homolog will be automatically assigned to functional categories using the MIPS functional catalog. All extracted proteins are in addition automatically analysed and annotated by the PEDANT suite.

Proper citation: MIPS Ustilago maydis Database (RRID:SCR_007563) Copy   

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http://topdb.enzim.hu

Collection of transmembrane protein datasets containing experimentally derived topology information from the literature and from public databases. Web interface of TOPDB includes tools for searching, relational querying and data browsing, visualisation tools for topology data.

Proper citation: Topology Data Bank of Transmembrane Proteins (RRID:SCR_007964) 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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https://web.uri.edu/riinbre/mic/

Core provides sequencing and bioinformatics support for INBRE and non-INBRE researchers. Provides data science services adjacent to traditional bioinformatics; access to computational and software resources for INBRE network institutions, particularly primarily undergraduate institutions; training for students and faculty in data science methods. Maintains professional network with other core and user facilities in Rhode Island and beyond to maximize resources available to our users.Utilizes novel technologies such as virtual/augmented reality for use in teaching and research.

Proper citation: Rhode Island INBRE Molecular Informatics Core Facility (RRID:SCR_017685) Copy   

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http://mgm.ku.edu/services

Research oriented service laboratory providing informatics support to research community. Services include data analysis and mining in proteomics, genomics and chemistry, systems biology approaches such as pathway, network and interaction analyses, large scale statistical and machine learning studies, protein structure, function and stability prediction, sequence and domain analyses,d esign and implementation of relational databases and software programs, consultation on experimental design involving data acquisition, management and analysis, report, grant, and manuscript preparation.

Proper citation: Kansas University at Lawrence Applied Bioinformatics Laboratory Core Facility (RRID:SCR_017751) Copy   

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http://genetics.group.shef.ac.uk/index.html

Core provides DNA sequencing services including DNA extraction, cell line identification, microsatellite analysis, and antibody sequencing,DNA Sequencing, Monoclonal Antibody Sequencing,Nucleic Acid Quantification,PCR Machine Hire,Real-Time PCR Robotic Liquid Handling,Taqman SNP Analysis.

Proper citation: University of Sheffield Genomic Core Facility (RRID:SCR_017912) Copy   

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https://github.com/DerrickWood/kraken2

Software tool as second version of Kraken taxonomic sequence classification system.

Proper citation: kraken2 (RRID:SCR_026838) Copy   

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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   

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https://github.com/SCANDAN-Team/SCANDAN-DICOM-labelling

Software tool for rules for DICOM tag based labelling. Regular expression used during the SCANDAN project to label MRI scans based on DICOM tag.

Proper citation: SCANDAN-DICOM-labelling (RRID:SCR_028365) Copy   

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http://www.xenbase.org/

Data collection for Xenopus laevis and Xenopus tropicalis biology and genomics.

Proper citation: Xenbase (RRID:SCR_003280) Copy   

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http://brainarray.mbni.med.umich.edu/Brainarray/Database/ProbeMatchDB/ncbi_probmatch_para_step1.asp

Matches a list of microarray probes across different microrarray platforms (GeneChip, EST from different vendors, Operon Oligos) and species (human, mouse and rat), based on NCBI UniGene and HomoloGene. The capability to match protein sequence IDs has just been added to facilitate proteomic studies. The ProbeMatchDB is mainly used for the design of verification experiments or comparing the microarray results from different platforms. It can be used for finding equivalent EST clones in the Research Genetics sequence verified clone set based on results from Affymetirx GeneChips. It will also help to identify probes representing orthologous genes across human, mouse and rat on different microarray platforms.

Proper citation: ProbeMatchDB 2.0 (RRID:SCR_003433) Copy   

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http://khavarilab.stanford.edu/resources.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. An intersection-based pathogen detection workflow that utilizes a user-provided custom reference genome set for identification of nonhuman sequences in deep sequencing datasets. This is a package recommended for advanced users only.

Proper citation: RINS (RRID:SCR_003652) Copy   

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http://www.cmhd.ca/genetrap/

Generate gene trap insertions using mutagenic polyA trap vectors, followed by sequence tagging to develop a library of mutagenized ES cells freely available to the scientific community. This library is searchable by sequence or key word searches including gene name or symbol, chromosome location, or Gene Ontology (GO) terms. In addition,they offer a custom email alert service in which researchers are able to submit search criteria. Researchers will receive automated e-mail notification of matching gene trap clones as they are entered into the library and database. The resource features the use of complementary second and third generation polyA trap vectors developed by the Stanford lab and the laboratory of Professor Yasumasa Ishida of the Nara Institute of Science and Technology (NAIST) in Japan to mutagenize murine embryonic stem (ES) cells. CMHD gene trap clones are distributed by the Canadian Mouse Mutant Repository(CMMR). Information about ordering, services, and pricing can be found on their web site (http://www.cmmr.ca/services/index.html)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

Proper citation: Centre for Modeling Human Disease Gene Trap Resource (RRID:SCR_002785) Copy   

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http://camera.calit2.net/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016; however, the URL provides links to associated projects and data. A suite of data query, download, upload, analysis and sharing tools serving the needs of the microbial ecology research community, and other scientists using metagenomics data.

Proper citation: Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (RRID:SCR_002676) Copy   

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http://www.hgsc.bcm.tmc.edu/content/honey-bee-genome-project

The HGSC has sequenced the honey bee, Apis mellifera. The version 4.0 assembly was released in March 2006 and published in October 2006. The genome sequence is being upgraded with additional sequence coverage. The honey bee is important in the agricultural community as a producer of honey and as a facilitator of pollination. It is a model organism for studying the following human health issues: immunity, allergic reaction, antibiotic resistance, development, mental health, longevity and diseases of the X chromosome. In addition, biologists are interested in the honey bee's social organization and behavioral traits. This project was proposed to the HGSC by a group of dedicated insect biologists, headed by Gene Robinson. Following a workshop at the HGSC and a honey bee white paper, the HGSC began the project in 2002. A 6-fold coverage WGS, BAC sequence from pooled arrays, and an initial genome assembly (Amel_v1.0) were released beginning in 2003. This has been a challenging project with difficulty in recovering AT-rich regions. The WGS data had lower coverage in AT-rich regions and BAC data from clones showed evidence of internal deletions. Additional reads from AT enriched DNA addressed these underrepresented regions. The current assembly Amel_4.0 was produced with Atlas and includes 2.7 million reads (1.8 Gb) or 7.5x coverage of the (clonable) genome. About 97% of STSs, 98% of ESTs, and 96% of cDNAs are represented in the 231 Mb assembly. About 2,500 reads were also produced from a strain of Africanized honey bee and SNPs were extracted. These were released in dbSNP and the NCBI Trace Archive. Analysis of the genome by a consortium of 20 labs has been completed. This produced a gene list derived from five different methods melded through the GLEAN software. Publications include a main paper in Nature and up to forty companion papers in Genome Research and Insect Molecular Biology. Sponsors: Sequencing of the honey bee is jointly funded by National Human Genome Research Institute (NHGRI) and the Department of Agriculture (USDA). Multiple drones from the same queen (strain DH4) were obtained from Danny Weaver of B. Weaver Apiaries. All libraries were made from DNA isolated from these drones. The honey bee BAC library (CHORI-224) was prepared by Pieter de Jong and Katzutoyo Osoegawa at the Children's Hospital Oakland Research Institute.

Proper citation: Honey Bee Genome Project (RRID:SCR_002890) Copy   

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http://rana.lbl.gov/drosophila

A single source for sequences, assemblies, annotations and analyses of the genomes of members of the fruitfly genus Drosophlia. It is meant as resource for Drosophilists and other researchers interested in comparative analysis of these species and their genomes. There are pages for each species, as well as pages for different types of multi-species resources (e.g. alignments). If you have a public resource that will help this project, please consider making it available through this page by emailing multiple_at_fruitfly.org.

Proper citation: Assembly/Alignment/Annotation of 12 Related Drosophila Species (RRID:SCR_002921) Copy   

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http://proteininformationresource.org/

Integrated public bioinformatics resource to support genomic, proteomic and systems biology research and scientific studies. Provides databases and protein sequence analysis tools to scientific community, including Protein Sequence Database which grew out from the Atlas of Protein Sequence and Structure. Conducts research in biomedical text mining and ontology, computational systems biology, and bioinformatics cyberinfrastructure. In 2002 PIR, along with its international partners, EBI (European Bioinformatics Institute) and SIB (Swiss Institute of Bioinformatics), were awarded a grant from NIH to create UniProt, a single worldwide database of protein sequence and function, by unifying the PIR-PSD, Swiss-Prot, and TrEMBL databases. Currently, PIR major activities include: i) UniProt (Universal Protein Resource) development, ii) iProClass protein data integration and ID mapping, iii) PRO protein ontology, and iv) iProLINK protein literature mining and ontology development. The FTP site provides free download for iProClass, PIRSF, and PRO.

Proper citation: Protein Information Resource (RRID:SCR_002837) Copy   

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http://www.hgsc.bcm.tmc.edu/content/red-flour-beetle-genome-project

This portal provides information about the Tribolium castabeum Genome Project. The Tribolium castaneum genome sequence and its analysis has been published in Nature, two companion journal issues (IBMB and DGE) and numerous other publications listed below. The red flour beetle, Tribolium castaneum, a common pest that is also a genetic model for the Coleoptera. The genome has been sequenced to 7-fold coverage using a whole genome shotgun approach and assembled using the HGSC's assembly engine, Atlas, with methods employed for the Drosophila pseudoobscura genome assembly. Approximately 90% of the genome sequence has been mapped to chromosomes in collaboration with Dick Beeman (USDA ARS) and Sue Brown (Kansas State University). Access to the Data :- Genome Assembly: The long term home of the Tribolium genome is Beetlebase. Tcas 3.0 is now available in GenBank and on our FTP site. Note there are no restrictions of any kind on the Tribolium data as it has been published. Version 2 of the assembly, Tcas_2.0 is available for download using the FTP Data link in the sidebar. The assembly is described in detail in the README in that directory. T.cas_1.0 was a preliminary genome assembly that did not include large insert paired end information and has been moved to a previous assemblies folder. A genboree browser of the Tcas2.0 sequence is available here: There are also links to the genboree browser from the blast results (at the bottom of each reported HSP) if you use the blast server on this page. The original linear scaffold file, Tcas2.0/linearScaffolds/Tcas20050914-genome, posted on the ftp site did not include singleton contigs from the assembly and thus did not fully reflect the tribolium genome sequence, missing ~4.4Mb of sequence in 1860 contigs and reptigs or approximately 2.5% of the assembled sequence. A corrected Tcas20051011-genome file containing these missing sequences is now available on the ftp site. The blast databases have also been updated to reflect this change. All other data is correct, and not affected by this change. :- BLAST Searches: The BLAST link is located in the sidebar. :* Linearized chromosome and unplaced scaffold sequences :* Assembled contigs :* Bin0 unassembled reads and Repeat reads Traces are available from the NCBI Trace Archive by using the link in the sidebar, or by using NCBI MegaBLAST with a same species or cross species query. Sponsors: Funding for this project has been provided by the National Human Genome Research Institute (NHGRI U54 HG003273), which is part of the National Institutes of Health (NIH), and the U.S. Department of Agriculture's Agricultural Research Service (USDA ARS Agreement No. 58-5430-3-338).

Proper citation: Tribolium castaneum Genome Project (RRID:SCR_002848) Copy   

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http://hapmap.ncbi.nlm.nih.gov/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A multi-country collaboration among scientists and funding agencies to develop a public resource where genetic similarities and differences in human beings are identified and catalogued. Using this information, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors. All of the information generated by the Project will be released into the public domain. Their goal is to compare the genetic sequences of different individuals to identify chromosomal regions where genetic variants are shared. Public and private organizations in six countries are participating in the International HapMap Project. Data generated by the Project can be downloaded with minimal constraints. HapMap project related data, software, and documentation include: bulk data on genotypes, frequencies, LD data, phasing data, allocated SNPs, recombination rates and hotspots, SNP assays, Perlegen amplicons, raw data, inferred genotypes, and mitochondrial and chrY haplogroups; Generic Genome Browser software; protocols and information on assay design, genotyping and other protocols used in the project; and documentation of samples/individuals and the XML format used in the project.

Proper citation: International HapMap Project (RRID:SCR_002846) Copy   

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http://hiv-web.lanl.gov/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023. HIV Sequence Database is a database of annotated HIV sequences, plus a variety of tools and information for researchers studying HIV and SIV. The main aim of this website is to provide easy access to our sequence database, alignments, and the tools and interfaces we have produced. The HIV Sequence Database focuses on five primary goals: * Collecting HIV and SIV sequence data (all sequences since 1987) * Curating and annotating this data, and making it available to the scientific community * Computer analysis of HIV and related sequences * Production of software for the analysis of (sequence) data * The data and analyses on this site and published in a yearly printed publication, the HIV sequence Compendium, which is available free of charge.

Proper citation: HIV Sequence Database (RRID:SCR_002906) Copy   

•   Source: SciCrunch Registry