Genomics

From MyBio

[edit] Categories which link here

[edit] Related subcategories

[edit] Genomics - Quick Links

GMOD		Genome Channel
UCSC Genome Bioinformatics		Bodymap
DoTS		XGI :: X Genome Initiative
euGenes		iCE - Contig Explorer
PINdb		Asterias

[edit] Genomics - Web Resources

Asterias includes applications for the analysis of genomic data that cover from data normalization to development of prediction models for survival data. Most of our applications use parallelization (via MPI) and run on a server with 60 CPUs for computation.

GMOD or the Generic Model Organism Database project is a largely open source project to develop a complete set of software for creating and administering a model organism database. Components of this project include genome visualization and editing tools, literature curation tools, a robust database schema, biological ontology tools, and a set of standard operating procedures. Affiliates include WormBase, FlyBase, Mouse Genome Informatics, Gramene, the Rat Genome Database, TAIR, EcoCyc, and the Saccharomyces Genome Database.

Genome Channel
SiteMap. Feedback. Life Sciences Division. ORNL. Disclaimer. Webmaster.

UCSC Genome Bioinformatics
This site contains the reference sequence for the human genome and working drafts for the mouse, rat, and SARS genomes

DPL Forum: Too few categories!

Bodymap
A databank of gene expression information of human and mouse genes, created by random sequencing of clones in 3'-directed cDNA libraries.
Data bank of expression information of human and mouse genes, novel or known, in various tissues or cell types and various timings. The first generation map was created by random sequencing. BodyMap is a human and mouse gene expression database that has been maintained since 1993. It is based on site-directed 3¹-ESTs collected from non-biased cDNA libraries constructed at Osaka University and contains more than 270, 000 sequences from 60 human and 38 mouse tissues. The site-directed nature of the sequence tags allows unequivocal grouping of tags representing the same transcript and provides abundance information for each transcript in different parts of the body. Our collection of ESTs was compared periodically with other public databases for cross referencing. The histological resolution of source tissues and unique cloning strategy that minimized cloning bias enabled BodyMap to support three unique mRNA based experiments in silico. First, the recurrence information for clones in each library provides a rough estimate of the mRNA composition of each source tissue. Second, a user can search the entire data set with nuleotide sequences or keywords to assess expression patterns of particular genes. Third, and most important, BodyMap allows a user to select genes that have a desired expression pattern in humans and mice.

DoTS
Database Of Transcribed Sequences. Human and mouse transcript index created from all publicly available transcript sequences. The input sequences are clustered and assembled to form the DoTS Consensus Transcripts that comprise the index.

XGI :: X Genome Initiative
The X Genome Initiative (XGI) is a comprehensive integrated system for the storage, analysis and visualization of DNA sequences. It was designed as a solution for high throughput expressed sequence tag (EST) and genomic sequencing operations that require professional bioinformatics support, either operating remotely or in-house. XGI is accessed in remote mode, with db and pipeline software behind firewall at NCGR, accessed by users via http or https, although it can be locally installed. XGI security features permit selective sharing of data among different user groups. XGI assists researchers by automating sequence processing and analysis operations, organizing sequences and results of analysis allowing intuitive interpretation. Once researchers deposit sequences at NCGR the analysis pipeline is applied to these sequences and users are able to explore sequences and the analytical results of the pipeline operations via internet.

euGenes
euGenes provides a common summary of gene and genomic information from eukaryotic organism databases. Catalogs gene symbol and full name, chromosome, genetic and molecular map information, gene product information (function, structure, and homologies), links to extended gene information.

iCE - Contig Explorer
Viewer for physical map data (for mouse, rat, cow, Cryptococcus) developed at the Genome Sciences Centre, Vancouver.

PINdb
Proteins Interacting in the Nucleus database. Proteins Interacting in the Nucleus database (PINdb) is a database of protein complexes purified from the nucleus of human and yeast cells. It is compiled from the published literature and existing databases. Currently, PINdb contains mostly protein complexes that may be involved in gene transcription. To facilitate comparative analyses and identification of protein complexes, the compositional information is integrated with standardized gene nomenclature, annotation and protein sequences from public databases. The PINdb web interface provides a number of tools for (1) comparison of protein complexes, (2) search for a protein complex by its published name or by a partial list of its components and (3) browsing specific subsets or a functional classification of the complexes.