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Links tagged with 'genetic markers'

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ARTSDatabase Content

http://andromeda.gsf.de/arts

DNA > Sequence Polymorphisms
Model Organisms > Mouse and Rat

ARTS (Advanced Retrieval Tool for SNPs) can be used to retrieve SNP that are polymorphic between several different mouse strains to aid in the design of genome-wide SNP marker panels.

NAR Web Server Issue 2005
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tagsanimals chromosome mapping genetic markers genomics genotype inbred c3h mice mice mutant strains mice single nucleotide polymorphism

DNannotatorTool Content

http://bioapp.psych.uic.edu/DNannotator.htm

DNA > Annotations
Human Genome > Annotations

DNannotator is a tool that performs de novo annotation of SNPs, STSs, and exons. It also allows for the migration of user-defined annotations onto different versions of genomic sequences (<30Kb size limit).

This content is being maintained by cliu.

NAR Web Server Issue 2003
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tagsalgorithms dna primers dna sequence analysis gene frequency genetic databases genetic markers genomics human chromosomes human genome humans sequence alignment sequence tagged sites single nucleotide polymorphism

FINDbaseDatabase Content

http://www.findbase.org

Human Genome > Databases

Frequency of INherited Disorders database (FIND base) records frequencies of causative genetic variations worldwide. Database records include the population and ethnic group or geographical region, the disorder name and the related gene, accompanied by links to any related external resources and the genetic variation together with its frequency in that population. Other features include: (i) the systematic collection and thorough documentation of population/ethnic group-specific pharmacogenomic markers allele frequencies for markers in genes of pharmacogenomic interest from different classes of drug-metabolizing enzymes and transporters, representing 150 populations and ethnic groups worldwide; (ii) the development of new data querying and visualization tools in the expanded FINDbase data collection that facilitates querying of large data sets and visualizing the results; and (iii) the establishment of the first database journal, by affiliating FINDbase with Human Genomics and Proteomics journal.

NAR Database Issue 2011
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tagsethnic groups gene frequency genetic markers genetic variation humans inborn genetic diseases nucleic acid databases periodicals as topic pharmacogenetics

G2DTool Content

http://www.ogic.ca/projects/g2d_2/

Human Genome > Health and Disease

G2D (Candidate Genes to Inherited Diseases) scans a human genomic region for genes related to an inherited disease. The G2D server also presents precomputed candidate genes for more than 600 genetically inherited diseases that have been mapped onto chromosomal regions without assignment of a particular gene.

NAR Web Server Issue 2007
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tagsalgorithms alzheimer disease asthma chromosome mapping computational biology genes genetic databases genetic linkage genetic markers genetic predisposition to disease human genome humans inborn genetic diseases mathematics medline obesity phenotype type 2 diabetes mellitus

GeMprospectorTool Content

http://cgi-www.daimi.au.dk/cgi-chili/GeMprospector/main

DNA > Tools For the Bench
Expression > cDNA, EST, SAGE
Model Organisms > Plants

GeMprospector is designed to find cross-species genetic marker candidates in legumes and grasses. GeMprospector automates PCR primer design based on multiple sequence alignments of submitted ESTs and their homologues in sequence databases from legumes or grasses.

NAR Web Server Issue 2006
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tagsbase sequence conserved sequence dna primers expressed sequence tags fabaceae genetic markers genetic polymorphism genomics nucleic acid databases poaceae polymerase chain reaction sequence alignment

Genome Database for RosaceaeDatabase Content

http://www.rosaceae.org/

DNA > Mapping and Assembly
Expression > cDNA, EST, SAGE
Model Organisms > Plants

Genome Database for Rosaceae (GDR) contains all publically available Rosaceae sequences including annotated peach, strawberry and almond EST sequences and the genetically anchored peach physical map.

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tagschromosome mapping expressed sequence tags genetic databases genetic markers genetics genomics plant genome research rosaceae sequence alignment systems integration

GenoWatchTool Content

http://genepipe.ngc.sinica.edu.tw/genowatch

Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms

A disease gene mining browser for association study. GenoWatch is a real-time batch SNP and short tandem repeat polymorphism pipeline that extracts current information from public domain websites such as NCBI, UniProt, KEGG and GO so that users can select the appropriate disease candidate genes.

NAR Web Server Issue 2008
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tagschromosome mapping genes genetic databases genetic markers genetic polymorphism human genome humans inborn genetic diseases microsatellite repeats pubmed single nucleotide polymorphism

ITS2Tool Content

http://its2.bioapps.biozentrum.uni-wuerzburg.de/

DNA > Phylogeny Reconstruction
RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

The Internal Transcribed Spacer 2 Database (ITS2) includes a homology based RNA structure prediction algorithm which allows the detection and secondary structure prediction of ITS2 sequences. This resource also contains more than 25,000 pre-calculated secondary structures for currently known ITS2 sequences that can be searched and browsed via taxonomy.

NAR Web Server Issue 2006
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tagsanimals base sequence computational biology conserved sequence eukaryota fungal genome fungi genetic databases genetic markers genetic transcription invertebrates molecular evolution molecular models molecular sequence data nucleic acid conformation nucleic acid databases nucleic acid sequence homology phylogeny plant genome plants ribosomal rna ribosomal spacer dna rna sequence analysis sequence alignment tertiary protein structure

NIASGBdbDatabase Content

http://www.gene.affrc.go.jp/databases_en.php

Model Organisms > Databases

The National Institute of Agrobiological Sciences Genebank Project database (NIASGBdb) consists of a genetic resource database and a plant diseases database, linked by a web retrieval database. The genetic resources database has plant and microorganism search systems to provide information on research materials, including passport and evaluation data for genetic resources with the desired properties. A database of plant diseases in Japan has been developed based on the listing of common names of plant diseases compiled by the Phytopathological Society of Japan. Relevant plant and microorganism genetic resources are associated with the plant disease names.

NAR Database Issue 2011
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tagsagricultural crops fungal dna fusarium genetic databases genetic markers genetic variation plant diseases

Rat Genome Database (RGD)Database Content

http://rgd.mcw.edu/

Model Organisms > Mouse and Rat

The Rat Genome Database (RGD) is a repository of rat genetic and genomic data. As well as integrating this data with mapping, physiological and strain information, RGD also provides researchers with several tools that facilitate searching, data mining and data analysis.

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tagsanimal disease models animals cardiovascular diseases chromosome mapping database management systems disease genetic databases genetic markers genetic variation genome genomics genotype heritable quantitative trait humans inborn genetic diseases inbred strains rats mice microsatellite repeats nervous system diseases nucleic acid databases phenotype quantitative trait loci radiation hybrid mapping rats sequence homology signal transduction systems integration terminology as topic

SALADDatabase Content

http://salad.dna.affrc.go.jp/salad/en/

Model Organisms > Databases
Protein > Databases

SALAD is a unique comparative genomics database from plant-genome-based proteome data sets. Evolutionarily conserved motifs were extracted by MEME software from protein-sequence annotation groups selected by BLASTP from the proteome data sets of 10 species: rice, sorghum, Arabidopsis thaliana, grape, a lycophyte, a moss, 3 algae, and yeast. Similarity clustering of each protein group was performed by pairwise scoring of the motif patterns of the sequences. The SALAD database provides a user-friendly graphical viewer that displays a motif pattern diagram linked to the resulting bootstrapped dendrogram for each protein group. Amino-acid-sequence-based and nucleotide-sequence-based phylogenetic trees for motif combination alignment, a logo comparison diagram for each clade in the tree, and a Pfam-domain pattern diagram are also available.

NAR Database Issue 2010
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tagsamino acid motifs computational biology genetic databases genetic markers genomics nucleic acid databases phylogeny plant genes plant genome plants protein databases species specificity

SEPACSTool Content

http://fred.bioinf.uni-sb.de/sepacs.html

Protein > Annotation and Function

SEPACS (Seroreactivity Pattern Classification System) is a a web-based application for classification of seroreactivity profiles.

NAR Web Server Issue 2007
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tagsalgorithms bayes theorem blood proteins brain neoplasms computational biology dna genetic markers glioma humans meningioma mutation neoplastic gene expression regulation oligonucleotide array sequence analysis sensitivity and specificity