Genomic Comparison Chart: Management and Analysis of Genomic Data
The following comparison table describes and compares the content of a series of websites that focus on a number of topics that are central to the management and interpretation of genomic, transcriptomic and proteomic data. These include information and/or tools that are valuable in considering: PCR methodology; SNPs; LD structure; genotyping and haplotyping; gene and genome sequence and structure; and gene expression. The various websites present a mixture of tools and data that are ready to be used. Bioconductor also provides an open source environment, based primarily on the R programming language, in which new tools can be developed and submitted for others.
| Genomic websites | Broad Institute Software | CLC Free Workbench | EBI | ENCODE project (for a part of the human genome only) | GeneSNPs | Genetic Associaiton Database | HapMap | NCBI | Seattle SNPs | UCSC | Bioconductor (open-source platform for software development) |
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| Link |
http://www.broad.mit.edu/ tools/software.html 
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http://www.clcbio.com/ index.php?id=28
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http://www.ebi.ac.uk
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http://genome.ucsc.edu/ ENCODE
http://www.hapmap.org/downloads/encode1.html.en
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http://www.genome.utah.edu/ genesnps
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http://geneticassociationdb.nih.gov
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http://www.hapmap.org/ index.html.en
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http://www.ncbi.nlm.nih.gov
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http://pga.gs.washington.edu
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http://genome.ucsc.edu/ index.html?org=Human& db=hg18&hgsid=116636913
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http://www.bioconductor.org/
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| Content: Link to other pages or websites | Many separate tools: Birdsuite, Arachne, Argo etc. | Many separate tools: ArrayExpress, Ensembl etc. | Link to NCBI, EBI | Link to OpenHelix, NCBI, UCSC, SeattleSNPs | Link to NCBI, UCSC, HapMap, HuGENavigator etc. | Link to NCBI | Many separate tools: Nucleotide, GEO etc. | Link to NCBI, HapMap, GVS/GeneSNPs | Link to Galaxy | Many separate tools | |
| Web-based Browsers : Genome; Proteome; SNPs; Structure; Pathway | Genome | Genome, Proteome, SNPs, Structure | Genome, Proteome, SNPs, Structure, Pathway | Genome, Proteome, SNPs, Structure, Pathway | Genome, Proteome, SNPs, Structure, Pathway | Genome | Genome, Proteome, SNPs, Structure | SNPs | Genome, Proteome | Genome | |
| Gene characteristics / structure Data (e.g: variants, exons, introns) |
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GWA karyogram |
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| Sequence data and tools (e.g: alignment blast) | Tools | Tools | Tools | Data | Tools | Tools & Data | Data | Tools & Data | Tools | Data | Tools |
| PCR Tools (e.g: in silico PCR, primers, cloning, design) |
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| PCR & Realtime PCR data |
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| Data and tools for Genotype / Haplotype / SNPs | Tools | Data | Data | Data | Data | Data | Data (ENCODE) | Data | Data | Data (ENCODE) | Tools |
| Data and tools for gene expression analysis (example of used techniques: microarrays, Western blot, Northern Blot) | Tools | Data (soon) | Data | Data | Data | Data | Data | Tools | |||
| Data and tools for Gene expression regulation analysis (example of used techniques: ChIP, RNAi, ChIP-ChIP) | Data | Tools | Tools & Data | Data | Data | Data | Data | Tools | |||
| LD, Phasing, QTL data |
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| Free access to Wet lab protocols | downloadable | available | available (GEO) | available | |||||||
| Gene functions (e.g: litterature review, interaction) |
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GWA karyogram |
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