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Bioinformatics


NCBI Genome Workbench

Although we are all familiar with the many public databases and tools at NCBI, there are many resources buried deep within the NCBI website that often go unknown to many. One of these gems is the Genome Workbench.
genomeworkbench1

As its name implies, Genome Workbench is an integrated, customizable application for viewing and analyzing sequence data. One of its strengths is its ability to import publically available sequence data and mash it up with your own imported private data. There is no online version of Genome Workbench. You must download and install the program onto your computer, which also means your private data stays private to your computing environment. Once you have downloaded it, run the Tutorial 1: Basic Operation, an excellent set of exercises which will acquaint you with the interface and options of the Workbench. You can follow the tutorials searches and data uploads, or substitute your own. A strong point of the Workbench is its full set of tutorials and practice datasets ranging from basic to advanced and include working with variation and alignments.

Some Genome Workbench Features:

  • Organizes data into Projects of your choosing (specific genes/sequences and their transcripts, regulatory elements, proteins, SNPs, STSs, etc.).
    • Projects are then collected into Workspaces (genes from different organisms, sequences correlated to a specific disease, your data chunks from the same organism, etc.)
  • Zoomable graphics mode.
    • Explore sequence data at different levels of detail, ranging from individual exons to genomic contexts, marching up and down chromosomes as needed.
  • View data as alignments, phylogenetic trees, graphically or as tables.
  • BLAST from within graphics mode.
  • Multiple options to align sequences including  ClustalW, MUSCLE.
  • Analyze variation, including SNPs.
  • Import Genome Wide Association Studies (GWAS) data.
  • Link-out service from within Workbench, including linking from sequences within Workbench to:
  • Click here to begin an immediate download of a NCBI PowerPoint presentation on the Genome Workbench which provides many more screenshots and a full overview.

Additional related links:

  • Genome Workbench FAQ, including the four mailing list servs that support it.
  • Help home page.

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