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Mouse and Rat

Resources include sequences, annotations, and comparative vertebrate genomics for mice and rats.

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Found 34 links

Displaying 15 links

Allen Brain AtlasDatabase Content

http://www.brain-map.org

Expression > cDNA, EST, SAGE
Model Organisms > Mouse and Rat

The Allen Brain Atlas (ABA) project has developed a web-based application designed to aid the intersection of neuroscience and genomics. The ABA Application enables users to access an extensive database of high resolution in situ hybridization (ISH) images from over 10,000 genes, reference atlases in both the sagittal and coronal planes, gene expression masks capturing the intensity of gene expression or signal, and the ability to search for gene expression by anatomic region.

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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

ASmodelerTool Content

http://genome.ewha.ac.kr/ECgene/ASmodeler/

Expression > Splicing
Model Organisms > Mouse and Rat
Sequence Comparison > Analysis of Aligned Sequences

Gene modeling server which focuses on the modeling of alternative splicing. It is based on the alignment of mRNA, EST and protein sequences and combines genome-based clustering and transcript assembly. Supports human, mouse and rat genomes.

NAR Web Server Issue 2004
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tagsalgorithms alternative splicing animals exons expressed sequence tags genetic models genome humans messenger rna mice molecular sequence data protein sequence analysis rats rna sequence analysis sequence alignment

BEARRTool Content

http://giscompute.gis.a-star.edu.sg/~vega/BEARR1.0/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Human Genome > Other Resources
Model Organisms > Mouse and Rat

Batch Extraction and Analysis of cis-Regulatory Regions (BEARR) takes a list of gene identifiers (such as RefSeq and Unigene IDs), consensus patterns, and (optionally) a position weight matrix as input and returns a list of matches for the patterns in both the sense and anti-sense strands of the relevant genomic sequence. The user specifies what distance up and downstream from both the transcription start site and the 3\' terminus to look for the patterns.

NAR Web Server Issue 2004
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tagsbinding sites dna dna sequence analysis gene expression profiling nucleic acid regulatory sequences oligonucleotide array sequence analysis software design transcription factors

ECR BrowserTool Content

http://ecrbrowser.dcode.org/

Model Organisms > Fish
Model Organisms > Fly
Model Organisms > Mouse and Rat
Model Organisms > Other Vertebrates
Sequence Comparison > Analysis of Aligned Sequences

The ECR (Evolutionary Conserved Regions) browser is a web-based tool for visualizing and navigating through whole genome alignments of several vertebrate species. Users can also submit sequences for alignment with one of the genomes represented.

NAR Web Server Issue 2004
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tagsanimals binding sites dna sequence analysis fishes genome genomics humans mice nucleic acid regulatory sequences rats sequence alignment synteny systems integration transcription factors

Ensembl Mouse Genome BrowserDatabase Content

http://www.ensembl.org/Mus_musculus/index.html

Model Organisms > Mouse and Rat

Analysis of finished and draft mouse genomic clone sequences.

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tagscomputational biology database management systems dna sequence analysis genetic databases human genome humans systems integration

Ensembl Rat Genome BrowserDatabase Content

http://www.ensembl.org/Rattus_norvegicus/

Model Organisms > Mouse and Rat

The Rat Genome project is an international collaboration to sequence the genome of the brown rat (Rattus norvegicus).

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tagscomputational biology database management systems dna sequence analysis genetic databases human genome humans systems integration

FANTOM - Functional Annotation of MouseDatabase Content

http://www.gsc.riken.go.jp/e/FANTOM/

Model Organisms > Mouse and Rat

Functional annotations for RIKEN full-length cDNA clones.

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tagsalgorithms animals chromosome mapping database management systems documentation genome mice phylogeny proteome sequence alignment sequence analysis systems integration transcription factors

GeneHub-GEPISTool Content

http://www.cgl.ucsf.edu/Research/genentech/genehub-gepis/

Expression > cDNA, EST, SAGE
Human Genome > Other Resources
Model Organisms > Mouse and Rat

GeneHub-GEPIS is a tool for inferring human and mouse gene expression patterns based on normalized EST abundance in various normal and cancerous tissues.

NAR Web Server Issue 2007
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tagsalgorithms biological tumor markers chromosome mapping dna sequence analysis expressed sequence tags gene expression profiling genetic testing humans neoplasms online systems sequence alignment

GeneMANIATool Content

http://www.genemania.org

Expression > Gene Set Analysis
Human Genome > Genomics
Model Organisms > Fly
Model Organisms > Mouse and Rat
Model Organisms > Plants
Model Organisms > Worm
Model Organisms > Yeast

GeneMANIA is web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Users input a query list for extension and weighting with functionally similar genes. Six organisms are supported.

This content is being maintained by baderg.

NAR Web Server Issue 2010
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tagsalgorithms animals computational biology factual databases gene regulatory networks genes genomics humans mice
setsUniversity of Toronto

IdiographicaTool Content

http://www.ncrna.org/idiographica/

DNA > DNA and Genomic Analysis
Human Genome > Other Resources
Model Organisms > Mouse and Rat

Idiographica is a general-purpose web application to build idiograms on-demand for human, mouse and rat. It allows users to generate high-quality idiograms with custom annotation according to their own genome-wide mapping/annotation data through an easy-to-use interface.

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tagsalgorithms animals chromosome banding chromosome mapping humans mice rats

LOCATEDatabase Content

http://locate.imb.uq.edu.au/

Model Organisms > Mouse and Rat
Protein > Localization and Targeting

LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of mouse proteins.

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tagsanimals membrane proteins mice protein databases protein isoforms proteome

Mammalian Gene CollectionDatabase Content

http://mgc.nci.nih.gov/

Expression > cDNA, EST, SAGE
Human Genome > Other Resources
Model Organisms > Mouse and Rat
Model Organisms > Other Vertebrates

Goal is to provide a complete set of full-length (open reading frame) sequences and cDNA clones of expressed genes for human and mouse; publicly accessible.

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tagsalgorithms animals base sequence complementary dna computational biology dna sequence analysis expressed sequence tags factual databases gene library genome human genome humans mammals mice national institutes of health (u.s.) open reading frames private sector public sector united states

Mouse Atlas of Gene ExpressionDatabase Content

http://www.mouseatlas.org/mouseatlas_index_html

Expression > cDNA, EST, SAGE
Model Organisms > Mouse and Rat

A quantitative and comprehensive atlas of gene expression in mouse development. The project has a goal of producing 150 publically available SAGE libraries.

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Mouse Genetics: Concepts and ApplicationsResource Content

http://www.informatics.jax.org/silver/

Model Organisms > Mouse and Rat

Online version of textbook by Lee Silver.

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Tags associated with subcategory 'Model Organisms/Mouse and Rat'

animals humans mice genomics algorithms rats genetic databases dna sequence analysis sequence alignment genome chromosome mapping computational biology database management systems systems integration proteins human genome missense mutation phylogeny peptide library signal transduction predictive value of tests genetic models exons tertiary protein structure protein databases terminology as topic genetic variation markov chains polymerase chain reaction genetic techniques dna primers chromosome banding automation biological tumor markers genetic testing messenger rna inborn genetic diseases biological evolution controlled vocabulary neoplasms online systems synteny protein sequence analysis factual databases expressed sequence tags dna transcription factors vertebrates genes human genome project inbred c3h mice mutant strains mice genotype species specificity molecular sequence data nucleic acid sequence homology software design oligonucleotide array sequence analysis cluster analysis conserved sequence binding sites neural networks (computer) rna sequence analysis fishes gene expression regulation genetic promoter regions gene expression profiling nucleic acid regulatory sequences california transcriptional regulatory elements genetic transcription protein binding molecular cloning single nucleotide polymorphism t-lymphocyte gene rearrangement brain nucleic acid databases genetic recombination comparative genomic hybridization dna copy number variations b-lymphocyte gene rearrangement data mining muscles radiation hybrid mapping sequence homology quantitative trait loci phenotype skin membrane proteins protein isoforms gene regulatory networks disease cardiovascular diseases heritable quantitative trait animal disease models untranslated rna national library of medicine (u.s.) pseudogenes reference standards inbred strains rats microsatellite repeats