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Lincoln Stein Makes Annotation Easy


Hanging out at the University of California, San Diego watering hole one evening during the Bioinformatics Open Source Conference, a young researcher from the Berkeley Drosophila Genome Project turned to his colleague and whispered with the kind of reverence generally reserved for rock stars, “Hey, that’s Lincoln Stein.”

Although Stein isn’t known for playing in a rock ‘n roll band, he has achieved celebrity status among bioinformaticists. The revolutionary Perl module he created for the Common Gateway Interface is considered one of the most widely used programs for creating Web applications.

These days Stein is working on a new project at the Cold Spring Harbor Laboratory that he said will enable researchers increased access to and understanding of genomic annotations.

“What happens is that the big sequencing centers publish large amounts of raw DNA data that goes into GenBank and then multiple groups take that and try to make some sense of it,” explained Stein. “Some are doing this by predicting genes, other people are lining cDNAs and expressed sequence tags to it to predict the regions that are transcribed to find alternative splicing patterns, and still others are doing experiments with it.”

“Now the problem is that it’s very difficult to integrate the results of these multiple independent annotation experiments because they are all using different terminology.”

In order to get everybody on the same page, Stein has developed the Distributed Sequence Annotation System, or DAS, a relatively simple language that allows researchers to describe the region of a genome they have studied in terms of coordinates. With everyone using the same coordinate system, understanding what several people may see happening at a particular point on a genome will be as easy as finding a particular street on a map.

“A biologist using a browser can ask what’s been done over a particular region and get precise answers so that he can compare (different studies),” said Stein, noting that the system would decentralize sequence annotation among multiple third-party annotators. Instead of resolving contradictions between different annotations, the system would actually allow users to compare notes.

How is all this done? Using the same underlying principle as Napster, the controversial software that gives Internet users the ability to swap music files.

Stein might be able to make it into the Rock and Roll Hall of Fame after all.

(For more information about DAS, go to

­--Jennifer Friedlin

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