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Initiative for Annotating Genomes Proposed 1/24/05

Mon, 01/24/2005 - 11:38am
A new report released by the American Academy of Microbiology recommends that a centralized genome annotation initiative be established in the United States. The group stated that not enough is being done to interpret the wealth of genomic data by assigning functions to sequenced genes.

"Roughly 40% of predicted genes have not been assigned even tentative functions. It is rare in science to be able to clearly delineate the boundaries of current knowledge, but that is exactly where genomics stands today," according to the report. "The annotation initiative proposed in this document will extend those boundaries and will likely lead to new applications and new progress in healthcare, biodefense, energy, the environment, and agriculture."

A key component of the initiative, they said, is the development of a centrally organized database of peer-reviewed, experimentally verified gene annotations, tied to catalogs of genes that have yet to be annotated and known biochemical functions for which a gene has yet to be found.

“Much of the currently available annotation information is provided by computer programs that predict the functions of newly sequenced genes on the basis of their similarity to genes of known (or predicted) function,” the report states.” This technique is inherently limited in both breadth and accuracy by the small size of the core foundational set of genes with experimentally established functions. By expanding that foundational set through a systematic program of biochemical study of genes of unknown function, we can dramatically increase the quality of prokaryotic genome annotations, and enhance our understanding of current and future genome sequences.”

Additionally, the report cites lack of available funding as a primary reason that progress in this field has been so slow. The report recommends that the new annotation initiative provide flexible funding to support experiments that will test annotation predictions, including nontraditional funding mechanisms such as smaller awards to a greater number of laboratories and awards to support student research.

The report is based on the findings of a colloquium convened by the Academy in Washington, D.C., in July 2004. Scientists, including microbiologists, biochemists, and bioinformatics specialists gathered to address the challenges of genome annotation and to seek ways to accelerate progress in the field of genome annotation.

By Elizabeth Tolchin


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