> > Other Vertebrates

Other Vertebrates

Links in this section include genomic databases and resources specific to other vertebrates.

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Cancer Genome Anatomy ProjectTool Content

http://cgap.nci.nih.gov/

DNA > Sequence Polymorphisms
Expression > cDNA, EST, SAGE
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Model Organisms > Other Vertebrates

Goal is to determine the gene expression profiles of normal, precancer, and cancer cells; resources for human and mouse include ESTs, gene expression patterns, SNPs, cluster assemblies, cytogenetic information, and tools to query and analyze the data.

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tagsgene library human genome project humans neoplasms

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 Human Genome BrowserDatabase Content

http://www.ensembl.org/Homo_sapiens/

Model Organisms > Other Vertebrates

Website, MySQL server and perl API access to software system which produces and maintains automatic annotation on eukaryotic genomes; uses NCBI assembly.

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

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

SOURCEDatabase Content

http://source.stanford.edu

DNA > Sequence Retrieval and Submission
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Human Genome > Other Resources
Model Organisms > Mouse and Rat
Model Organisms > Other Vertebrates
Protein > Sequence Retrieval

Stanford Online Universal Resource for Clones and ESTs pools publicly available data commonly sought for any clone, GenBank accession, or gene from human, mouse, rat.

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tagsanimals chromosome mapping dna-binding proteins gene expression profiling genetic databases genomics humans mice neoplasm antigens oligonucleotide array sequence analysis proteins rats type ii dna topoisomerases

TCAG: The Centre for Applied Genomics, TorontoResource Content

http://www.tcag.ca/

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

The Centre for Applied Genomics is a Canadian centre for human genome and disease research. Resources include Genomic and cDNA library screening (human, mouse, dog, pig) provided free to Canadian academic researchers with a nominal clone retrieval fee. Also: Research Genetics, NIA/NIH and RIKEN cDNAs.

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TFM-ExplorerTool Content

http://bioinfo.lifl.fr/TFM

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Gene Set Analysis
Human Genome > Annotations
Model Organisms > Fly
Model Organisms > Mouse and Rat
Model Organisms > Other Vertebrates

TFM-Explorer web server is a toolbox for the identification of putative transcription factor binding sites within a set of upstream regulatory sequences for a given set of genes. Only for human, mouse, rat, chicken and drosphila.

NAR Web Server Issue 2010
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tagsanimals binding sites brain data mining genomics humans mice muscles rats skin transcription factors transcriptional regulatory elements

TIGR Gene IndicesTool Content

http://compbio.dfci.harvard.edu/tgi/

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

An analysis of a set of unique, highly accurate virtual transcripts that are represented in the worlds public EST data; can perform a BLAST search against the TIGR unique Gene Indices.

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tagsanimals base sequence database management systems dna expressed sequence tags factual databases genes human genome project humans molecular sequence data nucleic acid sequence homology sequence alignment species specificity

UCSC Human Genome Browser GatewayTool Content

http://genome.ucsc.edu/cgi-bin/hgGateway?org=Human&db=0&hgsid=27735471

DNA > Annotations
Human Genome > Annotations
Model Organisms > Other Vertebrates

Provides a rapid and reliable display of any requested portion of the human genome at any scale, together with dozens of aligned annotation tracks.

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tagsanimals california database management systems genetic databases genomics human genome humans mice

Vega Annotation BrowserTool Content

http://vega.sanger.ac.uk

Human Genome > Annotations
Model Organisms > Fish
Model Organisms > Mouse and Rat
Model Organisms > Other Vertebrates

In collaboration with the genome sequencing centres, Vega attempts to present consistent high-quality curation of finished sequence.

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tagsanimals chromosome mapping dna sequence analysis genetic databases vertebrates

Tags associated with subcategory 'Model Organisms/Other Vertebrates'

humans animals mice dna sequence analysis genetic databases genomics human genome rats database management systems synteny systems integration transcription factors california neoplasms gene library human genome project molecular sequence data nucleic acid sequence homology sequence alignment genes factual databases nucleic acid regulatory sequences vertebrates dna expressed sequence tags genome species specificity dna-binding proteins gene expression profiling neoplasm antigens oligonucleotide array sequence analysis transcriptional regulatory elements skin algorithms binding sites brain muscles data mining proteins type ii dna topoisomerases united states base sequence chromosome mapping fishes public sector private sector complementary dna computational biology mammals open reading frames national institutes of health (u.s.)