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Boechera Microsatellite Website
Archives over 100,000 microsatellite allele calls from 4471 specimens of Boechera (Brassicaceae) (including 133 nomenclatural types). Boechera Microsatellite Website allows users to search and retrieve basic metadata using the Extrac# (a unique ID number annotated on every voucher specimen), taxon name, or locality. Searches based on taxon name can be limited to sexual diploids or expanded to include all hybrids containing that genome. The output of a taxon query can be used to produce working state and county level distribution lists free of the misidentifications common in other on-line resources. In addition to the basic search and display functions, Boechera Microsatellite Website also includes two algorithms: “Taxon Enquiry based on Similarity of Loci and Alleles” (TESLA) for sample identification, and “Parental Relationship Identification Using Subtraction” (PRIUS) for inferring the genomic constitution of hybrid individuals.
STaRRRT / Short Tandem Repeats in Regulatory Regions Table
Obsolete
Identifies tandem repeats in the regulatory region of genes. STaRRRT is a table that acts as a starting point for researchers interested in looking at the role of short tandem repeats (STRs) in promoter regions throughout the human genome. This resource is suitable for researchers with limited bioinformatics experience who are interested in specific STRs, genes or phenotypes. Multiple database identifiers are available, including Affymetrix array probe set identifiers.
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The Microorganisms Tandem Repeats Database
An internet-based resource to help develop and perform tandem repeats based bacterial strain typing. The tools comprise four parts. The Tandem Repeats Database enables the identification of tandem repeats across entire genomes. The Strain Comparison Page identifies tandem repeats differing between different genome sequences from the same species. The "Blast in the Tandem Repeats Database" facilitates the search for a known tandem repeat and the prediction of amplification product sizes. The "Bacterial Genotyping Page" is a service for strain identification at the subspecies level.
TRDB / Tandem Repeats DataBase
Provides information on tandem repeats in genomic DNA and tools for their analysis. TRDB consists of two parts: (i) a web accessible, public repository of information on the presence and characteristics of tandem repeats in a variety of genomes, and (ii) a research workbench which could serve as a model for future biological database development. A variety of tools, built into TRDB, simplify the study of repeats. It also provides data visualization features.
ChloroMitoSSRDB
A comprehensive online database of all SSRs (Simple Sequence Repeats) or STRs (Short Tandem Repeats) or Microsatellites from all sequenced Chloroplast and Mitochondrial genomes available so far across all the clades of life. SSRs are considered as important genomic elements and play a major role in the understanding the underpinnings of the evolution, linkage analysis and species discrimination. ChloroMitoSSRDB 2.0 provides a wide accessible platform for accessing the microsatellites patterns using the IMEx (Imperfect Microsatellite Extractor) and MISA and along with the primer pair information for the same. Additionally, the present version of the web-servers also allows the users to analyze the whole genome, genes and also NGS reads for the identification of the SSRs.
PMDBase / plant microsatellite DNAs database
A database to study microsatellite DNAs and marker development in a wide range of plant species and genome evolution. InPMDBase, 26,230,099 microsatellite DNA entries were identified among 110 genome sequenced plant species. For 81 species, genomic features of the microsatellite DNAs (genic or non-genic) were supplied with the corresponding genes or transcripts from public databases. Microsatellite DNAs can be explored through browsing and searching modules with a user-friendly web interface and customized software.
UgMicroSatdb / Unigene MicroSatellite database
A web-based relational database of microsatellites present in unigene sequences covering 80 genomes. UgMicroSatdb allows microsatellite search using multiple parameters like microsatellite type (simple perfect, compound perfect and imperfect), repeat unit length (mono- to hexa-nucleotide), repeat number, microsatellite length and repeat sequence class. Microsatellites can also be retrieved by specifying EST, cDNA, CDS identity or by using Gene Index, GenBank, UniGene IDs. The database also provides information about trinucleotide repeats encoding various amino acids. Such codon repeats can be searched by specifying characteristics of coded amino acids like charge (basic, acidic or neutral), polarity (polar or nonpolar), and their hydrophobic or hydrophilic nature. The nucleotide sequences of the target UniGenes are also provided to facilitate primer designing for PCR amplification of the desired microsatellite.
SNPSTR / microsatellite marker and tightly linked SNPs
Provides inferable single nucleotide polymorphisms short tandem repeats (SNPSTRs) for five model species: Homo sapiens, Mus musculus, Rattus norvegicus, Canis familiaris and Gallus gallus. SNPSTR contains more than 1700 000 SNPSTRs, shared in about 570 000 gene regions. For each entry, the database gives a database ID, species and chromosome where it is found, genomic start and end coordinates, microsatellite information, SNP information, information on gene when SNPSTR is in gene area, accession number of nearest OMIM disease where applicable and finally the sequence of the SNPSTR.
TRbase
Provides a platform to study the associations between disease genes and previously uncharacterized tandem repeats which is a key to understanding the mechanisms of pathogenicity of such diseases. These associations, together with the data indicating distribution patterns in protein-coding and non-coding regions can help direct future research into identifying the evolutionary history and functional significance of tandem repeats. In contrast to other available databases, TRbase identifies both perfect and imperfect repeats of 1-2000 bp unit lengths.
MitoSatPlant
Provides information about perfect, imperfect and compound Simple Sequence Repeats (SSRs). MitoSatPlant is an online resource of plant mitochondrial SSRs (mtSSRs). Additionally, Polymerase Chain Reaction (PCR) primers, statistical information such as density, average length of SSRs, frequencies of repeat type are also available. User can freely download the data available in this database which will help researchers to screen polymorphic markers in plant mitochondrial DNA.
CmMDb / The Cucumis melo L. microsatellite database
The first whole genome based microsatellite DNA marker database of Cucumis melo L. and comprehensive web resource that aids in variety identification and physical mapping of Cucurbitaceae family. The Cucumis melo L. microsatellite database encompasses 39,072 SSR markers along with its motif repeat, motif length, motif sequence, marker ID, motif type and chromosomal locations. The database is featured with novel automated primer designing facility to meet the needs of wet lab researchers. CmMDb is a freely available web resource that facilitates the researchers to select the most appropriate markers for marker-assisted selection in melons and to improve breeding strategies.
MMDBJ / Mouse Microsatellite Data Base of Japan
Accumulates data on genetic variations of microsatellite loci in Japanese wild mice-derived inbred strains, MSM and JF1. MMDBJ is an online resource that provides information about Simple Sequence Length Polymorphisms (SSLPs) among different mouse strains, focusing on strains derived from Japanese wild mouse. These data will be useful for clarifying the genetic backgrounds of the inbred strains as well as linkage analysis and positional cloning.
ChloroSSRdb
Provides information of all the three types (perfect, imperfect and compound) of simple sequence repeats (SSRs). In accordance with the growing interest in SSR studies, ChloroSSRdb will prove to be a useful resource in developing genetic markers, phylogenetic analysis, genetic mapping, etc. Moreover, it will serve as a ready reference for mined SSRs in available chloroplast genomes of green plants. ChloroSSRdb is a relational database developed using SQL server 2008 and accessed through ASP.NET.
OGDD / Olive Genetic Diversity Database
It is a genetic, morphologic and chemical database of worldwide olive tree and oil having a double function. In fact, besides being a reference system generated for the identification of unkown olive or virgin olive oil cultivars based on their microsatellite allele size(s), it provides users additional morphological and chemical information for each identified cultivar. Currently, OGDD is designed to enable users to easily retrieve and visualize biologically important information (SSR markers, and olive tree and oil characteristics of about 200 cultivars worldwide) using a set of efficient query interfaces and analysis tools. Compared with other few existing databases for olive species, OGDD has its own specific features and advantages. In fact, it provides a reference system in evaluating the data obtained from the analysis of unknown samples and in defining the varietal composition of the virgin olive oil. It also contains a great deal of information for each cultivar identified by the user. This database can be used by all researchers and stakeholders interested in olive cultivar identification and virgin olive oil authentication.
PTGBase
A public database to collect plant genes generated by tandem duplication mechanism in the process of plant evolution. PTGBase delivers the most comprehensive resource available to date, spanning 39 plant genomes, including model species and newly sequenced species alike. Across these genomes, 54 130 tandem duplicated gene clusters (129 652 genes) are presented in the database. Each tandem array, as well as its member genes, is characterized in complete detail. Tandem duplicated genes in PTGBase can be explored through browsing or searching by identifiers or keywords of functional annotation and sequence similarity. Users can download tandem duplicated gene arrays easily to any scale, up to the complete annotation data set for an entire plant genome. PTGBase will be updated regularly with newly sequenced plant species as they become available.
Ricebase
An integrative genomic database for rice (Oryza sativa) with an emphasis on combining datasets in a way that maintains the key links between past and current genetic studies. Ricebase includes DNA sequence data, gene annotations, nucleotide variation data and molecular marker fragment size data. The combined capabilities of Ricebase link genetic markers, genome context, allele states across rice germplasm and potentially user curated phenotypic interpretations as a community resource for genetic discovery and breeding in rice.
SBMDb / SugarBeet Microsatellite Marker Database
Using a computationally intensive in silico approaches, we mined and catalog the 145 K short tandem repeats (STR) markers and built the first whole genome based STR database. With the marker information present in the SBMDb, the linkage map’s marker density can be increased which will facilitate in QTL and gene mapping. In order to facilitate the use of these markers in various molecular breeding and QTL programs, we have implemented several plug-in to generate primers at user defined chromosomal locations, which can be directly exported for genotyping assays. SBMDb presents wide source of potential markers for developing and implementing new approaches for molecular breeding required to accelerate industrious use of this crop, especially for sugar, health care products, medicines and color dye. Identified markers will also help in improvement of bioenergy trait of bioethanol and biogas production along with reaping advantage of crop efficiency in terms of low water and carbon footprint especially in era of climate change.
HeteroGenome
Collects latent periodicity regions (with periods up to 2000 bp) revealed by the SS-approach in the genomes of various organisms. Tandem repeats and highly divergent tandem repeats along with the regions of a new type of periodicity, known as profile periodicity, have been collected for the genomes of Saccharomyces cerevisiae, Arabidopsis thaliana, Caenorhabditis elegans and Drosophila melanogaster. HeteroGenome is useful for both functional genomics and evolutionary genomics in searching for tandem repeats characteristic of the genome and for further research into the phenomenon of latent periodicity in DNA sequences. The database has a user-friendly interface and options for additional data analysis and allows query results to be downloaded.
TGRD / Tomato Genomic Resources Database
Obsolete
Allows interactive browsing of tomato genes, micro RNAs, simple sequence repeats (SSRs), important quantitative trait loci and Tomato-EXPEN 2000 genetic map altogether or separately along twelve chromosomes of tomato in a single window. TGRD is created using sequence of the cultivar Heinz 1706. High quality single nucleotide polymorphic (SNP) sites between the genes of Heinz 1706 and the wild tomato S. pimpinellifolium LA1589 are also included. Genes are classified into different families. 5'-upstream sequences (5'-US) of all the genes and their tissue-specific expression profiles are provided. Sequences of the microRNA loci and their putative target genes are catalogued. Genes and 5'-US show presence of SSRs and SNPs. SSRs located in the genomic, genic and 5'-US can be analysed separately for the presence of any particular motif. Primer sequences for all the SSRs and flanking sequences for all the genic SNPs have been provided. TGRD is a user-friendly web-accessible relational database and uses CMAP viewer for graphical scanning of all the features.
CGKB / Cowpea Genespace/Genomics Knowledge Base
Obsolete
Leverages modern molecular genetic tools for gene discovery and cowpea improvement. CGKB is an integrated and annotated resource for cowpea genespace sequences (GSS) with features of homology-based and Hidden Markov Model (HMM)-based annotations, enzyme and pathway annotations, gene ontology (GO) term annotation, toolkits, and a large number of other facilities to perform complex queries. The cowpea GSS, chloroplast sequences, mitochondrial sequences, retroelements, and simple sequence repeat (SSR) sequences are available as FASTA formatted files and downloadable.
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