Monday, August 28, 2000

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Scientific American Beyond the First Draft
"Unprecedented fanfare greeted the June 26 announcement that scientists had completed a draft of the human genome sequence. The truth is, however, that figuring out the order of the letters in our genetic alphabet was the easy part. Now comes the hard part: deciphering the meaning of the genetic instruction book.

The next stage goes by a deceptively prosaic name: annotation. Strictly speaking, "annotation" comprises everything that can be known about a gene: where it works, what it does and how it interacts with fellow genes. Right now, scientists often use the term simply to signify the first step: gene finding. That means discovering which parts of a stretch of DNA belong to a gene and distinguishing them from the other 96 percent or so that have no known function, often called junk DNA.

Several companies have sprouted up to provide bioinformatics tools, software and services [see "The Business of the Human Genome," Scientific American, July]. Their success, though, may hinge on a peaceful spot south of England's University of Cambridge. It is home to the Sanger Center, the U.K. partner in the publicly funded Human Genome Project (HGP) consortium, and the European Bioinformatics Institute (EBI), Europe's equivalent of the National Center for Biotechnology Information (NCBI) at the National Institutes of Health. Sanger and EBI are collaborating on the Ensembl project, which consists of computer programs for genome analysis and the public database of human DNA sequences. New DNA sequences arrive in bits and pieces; automated routines scan the sequences, looking for patterns typically found in genes. "One of the important things about Ensembl is that we're completely open, so you can see all our data, absolutely everything," says EBI's Ewan Birney." [via bioinformatics.org]

redux [07.25.00]
The Scientist Automatic annotations of the human genome will produce different interpretations
[requires 'free' registration]
"To translate the billions of sequenced bases of the human genome into meaningful information, investigators in the private and public sectors continue to use computer prediction to automatically annotate the human genome--to attach biological footnotes about genes, the proteins they encode, and the ailments to which they may be linked. But as with any translation, there's potential for multiple interpretations. Annotation projects could present geneticists with significantly different genome schematics.

"I think that for the moment scientists are going to have to revel in the variety," maintains Robert Waterston, director of the genome sequencing center at Washington University in St. Louis. A joint effort in the United Kingdom from the European Bioinformatics Institute (EBI) and the Sanger Centre, U.S. efforts at the National Center for Biotechnology Information (NCBI) and Oak Ridge National Laboratory (ORNL), and commercial efforts will present different annotations based on the data available, algorithms employed, and weight given to different data points. "

redux [06.23.00]
Guardian Unlimited Genome project recruits the world
"Bioinformatics is the science of life as a software problem. An international co-operation called the Human Genome Project is about to finish putting the human DNA blueprint on the internet.

And a team working closely with them is about to distribute a software package that will turn the world of biology into a co-operative research laboratory. The exploration of the human software will become a kind of global interactive game, with a new tool called Ensembl."

Tools The Ensembl Project
"Ensembl provides complete and consistent annotation across the human genome. It will soon also process mouse, (in conjunction with other projects, hopefully people like the Jackson Lab). To understand how Ensembl fits into the human genome project, please read EnsemblHGP"

"A central element of the Ensembl project is openness: all data is freely available; all code is freely available. You can read about the EnsemblSoftwareDesign and about how to DownloadEnsembl software and data and how to go about InstallingEnsembl on your own site in our developers area. You can follow Ensembl announcements, user discussion or development issues via a number of mailing lists as well as view previous emails here."

redux [04.24.00]
Eurekalert! Genome annotation experts take standardized test
"Now that the age of the genome is upon us, scientists must find a way to spin mountains of DNA code into biological gold. To do it, they are building their own Rumpelstiltskins: powerful computer programs that automatically scrutinize the code and decipher its genetic elements. The April issue of Genome Research reports a new enterprise to test the state of the art in computer "genome annotation." Organized by a team from University of California, Berkeley, 12 international groups compared the power of their computer programs to predict gene elements within a 3 million base pair stretch of Drosophila DNA.

The groups compared the results of their programs against each other and against the results of an exhaustive experimental and computational effort to locate all the genes in this region (not available to the participants during the test).

When the results were in, many programs had detected the genes in the region with 95% accuracy compared to the experimental effort. Furthermore, the programs made predictions of genes that had not been found in that effort, which researchers are now investigating. However, the programs were less accurate in defining the exact boundaries of the genes within the code, and groups that attempted to find elements controlling gene activity (e.g., promoters) made a large number of false predictions."