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These are some of the Genomics Websites endorsed by the Genomics Core of the Center for Neuroscience Research:

Resources available at the core are marked by

Resource

Description

Genomic Resources:

 

UCSC Genome Browser

This site contains the reference sequence and working draft assemblies for a large collection of genomes. It also provides a portal to the ENCODE project.

ENSEMBL

Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. Ensembl is primarily funded by the Wellcome Trust.

NCBI Entrez

An unified web base to query all the databases and resources available at the NCBI.

 

 

Next Generation Sequencing:

 

Bioinformatics for Next Generation Sequencing

Web page maintained by "Bioinformatics Journal"  containing the very latest papers in this area to help researchers keep abreast of the latest developments

 

 

Sequence Analysis:

 

DCODE.org

Dcode Comparative Genomics Center is a publicly available resourse for regulatory genome data mining. It provides tools for evolutionary comparisons, sequence alignments, and detection of functional sequence patterns.

TRANSFAC

TRANSFAC - the internationally unique knowledge base - contains data on transcription factors, their experimentelly-proven binding sites, and regulated genes. Its broad compilation of binding sites allows the derivation of positional weight matrices.

JASPAR

The JASPAR CORE database contains a curated, non-redundant set of 123 profiles, derived from published collections of experimentally defined transcription factor binding sites for multicellular eukaryotes. The prime difference to similar resources (TRANSFAC, TESS etc) consist of the open data acess, non-redundancy and quality: JASPAR CORE is a smaller set that is non-redundant and curated

Geneious

Geneious Pro is an integrated, cross-platform bioinformatics software suite for manipulating, finding, sharing, and exploring biological data such as DNA sequences or proteins, phylogenies, 3D structure information, publications, etc. It features sequence alignment and phylogenetic analysis, contig assembly, primer design and restriction analysis, access to NCBI and UniProt, BLAST, protein structure viewing, automated PubMed searching, and more. It even includes an API for creating your own plugins. It is free for academic users but donations are encouraged by the developers.

 

 

Batch Analysis:

 

UCSC Table Browser

Retrieve data associated with a UCSC genome track in text format to calculate intersections between tracks, and to extract DNA sequences covered by rthe track,.

Biomart

A web interface to query and download data in bulk from the various genomic resources developed by ENSEMBL, RGD and other resources.

 

 

Gene Expression Analysis:

 

GenePattern

GenePattern offers a toolbox of over 90 genomic and proteomic analysis tools, all of which are easily accessible through a powerful web interface.

Bioconductor

Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data. It is particularly powerful to carry out microarray data analysis.
The "Microarray Analysis with R & BioConductor" at UC Riverside by Thomas Girkhe is full of scripts and ideas for many different types of analysis with
R.

Cluster

Cluster and TreeView are an integrated pair of programs for analyzing and visualizing the results of complex microarray experiments

MultiExperiment Viewer

Normalized and filtered expression files can be analyzed using TIGR Multiexperiment Viewer (MeV). MeV is a versatile microarray data analysis tool, incorporating sophisticated algorithms for clustering, visualization, classification, statistical analysis and biological theme discovery.

GeneSpring GX

GeneSpring GX is a powerful visualization and analysis solution designed for use with expression data. Regarded as the gold standard in desktop expression analysis, GeneSpring GX allows researchers to identify targets quickly and reliably. By providing statistically meaningful results, GeneSpring GX enables prediction of clinical outcomes and characterization of novel expression patterns. GeneSpring GX is part of an integrated analysis suite that enables visual and analytical comparisons between expression, genotyping, protein, metabolite, and other data types to answer complex biological questions.

dChip

PC based software for analysis and visualization of gene expression and SNP arrays.

Gene Set Enrichment Analysis

Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes).

 

 

Pathways:

 

Ingenutiy Pathway Analysis

Web based platform to analyze the interaction and network structure of given list of genes/protein. It is based on extensive hand-curated literature information.  Email Lax Iyer or Chris Parkin for access. (lax.iyer@tufts.edu or christopher.parkin@tufts.edu)  

Reactome

A curated knowledgebase of biological pathways.

KEGG Pathway Database

Wiring diagram of molecular interactions, reactions and relations.

David Bioiformatics Resource

David is a poweful web based tool to Functional Annotation, Gene Classfication, Gene ID conversion for given list of genes.

 

 

GeneCards

GeneCards is an integrated database of human genes that includes automatically-mined genomic, proteomic and transcriptomic information, as well as orthologies, disease relationships, SNPs, gene expression, gene function, and service links for ordering assays and antibodies.

 

 

Neuroscience Related 

 

Biomedical Informatics

It is a geographically distributed virtual community of shared resources offering tremendous potential to advance the diagnosis and treatment of disease.

The Mouse Biomedical Informatics

MBAT is a collaborative effort by groups in the Mouse BIRN to create an interoperable toolkit that offers an intuitive way to access the functionality offered at the various institutions within the MBIRN Network. The goal of the MBAT is to act as an intuitive, interoperable interface for viewing, accessing, processing, and analyzing multimodal data with emphasis on functionality across distributed locations and diverse databases.  This tool MBIRNallows a user to view their data and offers the ability to interface with data offered by Mouse BIRN.

 

 

Bioinformatics World

A collection of evaluated bioinformatics programs and databases.

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