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http://bioinfo.unl.edu/raiphy.php

A semi-supervised metagenomic fragment classification software program that utilizes the genome signatures to characterize the DNA sequences and taxonomic classification is based on an information theoretic measure referred as Relative Abundance Index (RAI). A DNA sequence of unknown source is classified and taxonomically labeled based on the phylogenetic profiles of the previously sequenced genomes. The profiles are iteratively updated using the unknown DNA sequences and the classification results. After a few cycles, the metagenome is classified into operational taxonomic units.

Proper citation: RAIphy (RRID:SCR_004720) Copy   

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http://www.arabidopsis.org

Database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every two weeks from the latest published research literature and community data submissions. Gene structures are updated 1-2 times per year using computational and manual methods as well as community submissions of new and updated genes. TAIR also provides extensive linkouts from data pages to other Arabidopsis resources. The data can be searched, viewed and analyzed. Datasets can also be downloaded. Pages on news, job postings, conference announcements, Arabidopsis lab protocols, and useful links are provided.

Proper citation: TAIR (RRID:SCR_004618) Copy   

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http://www.genedb.org/Homepage/Lmajor

Database of the most recent sequence updates and annotations for the L. major genome. New annotations are constantly being added to keep up with published manuscripts and feedback from the Trypanosomatid research community. You may search by Protein Length, Molecular Mass, Gene Type, Date, Location, Protein Targeting, Transmembrane Helices, Product, GO, EC, Pfam ID, Curation and Comments, and Dbxrefs. BLAST and other tools are available. Leishmania species cause a spectrum of human diseases in tropical and subtropical regions of the world. We have sequenced the 36 chromosomes of the 32.8-megabase haploid genome of Leishmania major (Friedlin strain) and predict 911 RNA genes, 39 pseudogenes, and 8272 protein-coding genes, of which 36% can be ascribed a putative function. These include genes involved in host-pathogen interactions, such as proteolytic enzymes, and extensive machinery for synthesis of complex surface glycoconjugates. The Pathogen Genomics group at the Wellcome Trust Sanger Institute played a major role in sequencing the genome of Leishmania major (see Ivens et al.) Details of the centres involved and which chromosomes they sequenced, are given. The sequence data were obtained by adopting several parallel approaches, including complete cosmid sequencing, whole chromosome shotguns and/or BAC sequencing/skimming. The Leishmania parasite is an intracellular pathogen of the immune system targeting macrophages and dendritic cells. The disease Leishmaniasis affects the populations of 88 counties worldwide with symptoms ranging from disfiguring cutaneous and muco-cutaneous lesions that can cause widespread destruction of mucous membranes to visceral disease affecting the haemopoetic organs. In collaboration with GeneDB, the EuPathDB genomic sequence data and annotations are regularly deposited on TriTrypDB where they can be integrated with other datasets and queried using customized queries.

Proper citation: GeneDB Lmajor (RRID:SCR_004613) Copy   

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http://www.ncbi.nlm.nih.gov/nucest

Nucleotide database as collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery.

Proper citation: Nucleotide database (RRID:SCR_004630) Copy   

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https://computation-rnd.llnl.gov/lmat/

Open-source software tool to assign taxonomic labels to as many reads as possible in very large metagenomic datasets and report the taxonomic profile of the input sample. The quick "single pass" analysis of every read allows read binning to support additional more computationally expensive analysis such as metagenomic assembly or sensitive database searches on targeted subsets of reads.

Proper citation: LMAT (RRID:SCR_004646) Copy   

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http://metaphyler.cbcb.umd.edu/

A taxonomic classifier for metagenomic shotgun reads, which uses phylogenetic marker genes as a taxonomic reference. The classifier, based on BLAST, uses different thresholds (automatically learned from the reference database) for each combination of taxonomic rank, reference gene, and sequence length. The reference database includes marker genes from all complete genomes, several draft genomes and the NCBI nr protein database.

Proper citation: MetaPhyler (RRID:SCR_004848) Copy   

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http://blast.ncbi.nlm.nih.gov/Blast.cgi

Web search tool to find regions of similarity between biological sequences. Program compares nucleotide or protein sequences to sequence databases and calculates statistical significance. Used for identifying homologous sequences.

Proper citation: NCBI BLAST (RRID:SCR_004870) Copy   

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http://www.pantherdb.org/

System that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in absence of direct experimental evidence. Orthologs view is curated orthology relationships between genes for human, mouse, rat, fish, worm, and fly., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PANTHER (RRID:SCR_004869) Copy   

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http://compbio.cs.toronto.edu/prism/

Software for split read (reads which span across a structrual variant -- SV ) mapping and SV calling from the mapping result. It is able to detect small insertions and abitrary size deletions, inversions and tandom duplications with the direction of discordant read pairs. PRISM_CTX is a tool for detecting inter-chromosome trans-location events.

Proper citation: PRISM - Pair Read Informed Split Mapper (RRID:SCR_004812) Copy   

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http://dgv.tcag.ca/dgv/app/home

Public repository that accepts direct submissions and provides archiving, accessioning and distribution of publicly available genomic structural variants, in all species. Variants are accessioned at the study and sample level, granting stable identifiers that can be used in publications. DGVa data is integrated with other EBI resources, including comprehensive EBI search and Ensembl genome browser. Exchanges data with companion database, dbVar, at National Center for Biotechnology Information.NOTE: since 2019 DGVa doesn't accept submissions. Please send the data for submission to European Variation Archive (EVA).

Proper citation: Database of Genomic Variants Archive (DGVa) (RRID:SCR_004896) Copy   

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http://smart.embl.de/

Software tool for identification and annotation of genetically mobile domains and analysis of domain architectures.

Proper citation: SMART (RRID:SCR_005026) Copy   

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http://hadvwg.gmu.edu/

The Human Adenovirus Type Classification coordinates the naming of candidate new types, prior to manuscript submission for peer review. This resource contains a method of submitting candidate HAdV, criteria for a new HAdV type, and a Serotyping tool, which displays all potential types corresponding to the query serotype entered by a user. The criteria are based on discussions at the International Adenovirus Meeting (Dobog��k, Hungary; 26-30 April, 2009) and the NIH Human Adenovirus Working Group Workshop (Bethesda, MD. USA; 3 February 2011), which are summarized in a Letter to the Editor.

Proper citation: Human Adenovirus Type Classification (RRID:SCR_005753) Copy   

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http://www.clipz.unibas.ch/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 20,2019.Database and analysis environment for experimentally determined binding sites of RNA-binding proteins. It supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins in order to identify the binding sites of these proteins. The functional annotation could be also applied to short reads resulting from other types of experiments such as mRNA-Seq, Digital Gene Expression, small RNA cloning, etc. The platform enables visualization and mining of individual data sets as well as analysis involving multiple experimental data sets. The platform can support collaborative projects involving multiple users and groups of users as well as public and private datasets.

Proper citation: CLIPZ (RRID:SCR_005755) Copy   

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http://www.nematodes.org/nematodegenomes/index.php/Main_Page

A collaborative wiki that collates information on completed, ongoing and planned genome and transcriptome sequencing projects on species from phylum Nematoda. The intention is to encourage genome sequencing across the diversity of the phylum Nematoda. Wiki includes: * Published complete nematode genomes: A dynamically generated table of all species for which the genome is published. * Nematode species with genomes in progress: A dynamically generated table of all species for which a genome project is underway. Users may add species to the list * Proposed nematode genome projects: To propose a species for genome sequencing, edit its species page, and set the genome project status to proposed. * BLAST server: Search a number of the nematode-genomes-in-progress with genes of your choice. Currently there are 12 draft genomes available... * Genomes with Data available: Genomes with data available for download. Users may add more data URLs to strain pages or update the URLs.

Proper citation: 959 Nematode Genomes (RRID:SCR_006068) Copy   

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http://oligogenome.stanford.edu/

The Stanford Human OligoGenome Project hosts a database of capture oligonucleotides for conducting high-throughput targeted resequencing of the human genome. This set of capture oligonucleotides covers over 92% of the human genome for build 37 / hg19 and over 99% of the coding regions defined by the Consensus Coding Sequence (CCDS). The capture reaction uses a highly multiplexed approach for selectively circularizing and capturing multiple genomic regions using the in-solution method developed in Natsoulis et al, PLoS One 2011. Combined pools of capture oligonucleotides selectively circularize the genomic DNA target, followed by specific PCR amplification of regions of interest using a universal primer pair common to all of the capture oligonucleotides. Unlike multiplexed PCR methods, selective genomic circularization is capable of efficiently amplifying hundreds of genomic regions simultaneously in multiplex without requiring extensive PCR optimization or producing unwanted side reaction products. Benefits of the selective genomic circularization method are the relative robustness of the technique and low costs of synthesizing standard capture oligonucleotide for selecting genomic targets.

Proper citation: OligoGenome (RRID:SCR_006025) Copy   

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http://db-mml.sjtu.edu.cn/ICEberg/

ICEberg is an integrated database that provides comprehensive information about integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome. An ICE contains three typical modules, integration and excision, conjugation, and regulation modules, that collectively promote vertical inheritance and periodic lateral gene flow. Many ICEs carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. ICEberg offers a unique, highly organized, readily explorable archive of both predicted and experimentally supported ICE-relevant data. It currently contains details of 428 ICEs found in representatives of 124 bacterial species, and a collection of >400 directly related references. A broad range of similarity search, sequence alignment, genome context browser, phylogenetic and other functional analysis tools are readily accessible via ICEberg. ICEberg will facilitate efficient, multidisciplinary and innovative exploration of bacterial ICEs and be of particular interest to researchers in the broad fields of prokaryotic evolution, pathogenesis, biotechnology and metabolism. The ICEberg database will be maintained, updated and improved regularly to ensure its ongoing maximum utility to the research community.

Proper citation: ICEberg (RRID:SCR_006026) Copy   

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http://www.ncbi.nlm.nih.gov/projects/gv/rbc/main.fcgi?cmd=init

The dbRBC database provides an open, publicly accessible platform for DNA and clinical data related to the human Red Blood Cells (RBC). A new bioinformatics resource, dbRBC, has been installed at the National Center of Biotechnology Information (NCBI). This resource combines the well established Blood Group Antigen Gene Mutation Database (BGMUT) with tools and interlinked resources developed at the NCBI. The main task of dbRBC is to provide access to publicly available genomic, protein and structural information linked to the red blood cell antigens. The site offers a number of resources: * BGMUT Database * Alignment Viewer * SBT Tool * Probe/Primer Resource * Typing Kit Interface * Obstacle

Proper citation: NCBI dbRBC (RRID:SCR_005959) Copy   

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http://hannonlab.cshl.edu/index.html

The Hannon laboratory comprises a broad spectrum of programs in small RNA biology, mammalian genetics and genomics. We study RNAi and related pathways in a wide variety of organisms to extract common themes that define both the mechanisms by which small RNAs act and the biological processes which they impact. Currently, we focus on microRNAs, endogenous siRNAs and piRNAs and their roles in gene regulation, cancer biology, stem cell biology and in defense of the genome against transposons. In collaboration with Steve Elledge (Harvard) and Scott Lowe (CSHL), we develop genome-wide shRNA tools for RNAi-based genetics in mammalian cells, and we are now producing similar collections of artificial microRNAs for Arabidopsis with Detlef Weigel (MPI), Dick McCombie (CSHL) and Rob Martienssen (CSHL) as part of the 2010 project (see 2010.cshl.edu). Our genomic efforts include the application of RNAi-based genetic screens to cancer biology and stem cells. We also make heavy use of next generation sequencing methodologies for probing small RNA populations, in part as a member of the ENCODE consortium (with Tom Gingeras, CSHL). Finally, we develop (with Dick McCombie) and apply focal re-sequencing methods for identifying disease relevant mutations, for probing the epigenetic landscape and for the study of human evolution.

Proper citation: CSHL - Hannon Lab (RRID:SCR_005982) Copy   

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http://www.cmhd.ca/

Multidisciplinary collaboration undertaking genome-wide mutagenesis to functionally annotate the mouse genome and develop new mouse models relevant to human disease. To achieve these goals two major research platforms are carried out: Gene trapping and ENU Mutagenesis. A new challenge is faced in the post-genomic era - the assignment of biological function to the human genome sequence and projecting that assignment into understanding of human health and disease. The Centre for Modeling Human Disease (CMHD) was established to take part in the worldwide initiative to address these challenges. At the CMHD, two fundamentally different, yet complimentary methods are employed to generate mutant mouse models of human disease: chemical mutagenesis by ethylnitrosourea (ENU), and gene trap insertional mutagenesis. The Centre contributes its resources to similar international efforts and is the first of its kind in Canada. The Center is also actively developing other mutagenic strategies including pharmacologic and genetic modifier screens to dissect disease pathways, and novel mutagenic techniques using embryonic stem cells. ENU Database * Statistics for Mouse Physiological Parameters * Search Mutants by Phenotype * Search Mutants by Heritability Gene Trap Database * Search by in vitro Expression Pattern * Search by Gene Trap Sequences CMHD Members Only (must register and login) * Search Mouse Line * Histopathology * Sperm, Tissue, Slide Archiving * CMHD Database Download CMHD Services * Phenotyping * Genetic Mapping * Pathology * Pathology Service Charges

Proper citation: CMHD - Centre for Modeling Human Disease (RRID:SCR_006101) Copy   

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http://www.gwascentral.org/

Publicly available database of summary level findings from genetic association studies in humans, including genome wide association studies (GWAS). Previously named HGBASE, HGVbase and HGVbaseG2P.

Proper citation: GWAS Central (RRID:SCR_006170) Copy   

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