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Paul Kitts Genome Assembly and Annotation Process
14. Genome Assembly and Annotation Process
Paul Kitts
Created: October 9, 2002
Updated: August 13, 2003
Summary
The primary data produced by genome sequencing projects are often highly fragmented and
sparsely annotated. This is especially true for the Human Genome Project [/
page.cfm?pageID as a result of its policy of releasing sequence data to the public
sequence databases every day (1, 2). So that individual researchers do not have to piece together
extended segments of a genome and then relate the sequence to genetic maps and known genes,
NCBI provides annotated assemblies of public genome sequence data. NCBI assimilates data of
various types, from numerous sources, to provide an integrated view of a genome, making it easier
for researchers to spot informative relationships that might not have been apparent from looking at
the primary data. The annotated genomes can be explored using Map Viewer (Chapter 20) to
display different types of data side-by-side and to follow links between related pieces of data.
This chapter describes the series of steps, the “pipeline”, that produces NCBI's annotated
genome assembly from data deposited in the public sequence databases. A variant of the
annotation process developed for the human genome is used to annotate the mouse genome, and
similar procedures will be applied to other genomes (Box 1).
NCBI constantly strives to improve the accuracy of its human genome assembly and annotation,
to make the data displays more informative, and to enhance the utility of our access tools. Each run
through the assembly and annotation procedure, together with feedback from outside groups and
individual users, is used to improve the process, refine the parameters for individual steps, and add
new features. Consequently, the details of the assembly and annotation process change from one
run to the
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