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Finishing Needed Autofinish


“Finishing” Needed Autofinish…

We were interested to read your article “Finishing at a Fraction of the Cost” (GT 5/03), but somewhat surprised that you did not mention the program Autofinish. Autofinish has the same capabilities (and many more) as the ones you mention for Dick McCombie’s software, but in addition, Autofinish has been published (see Gordon, D., C. Desmarais, and P. Green. 2001. Automated Finishing with Autofinish. Genome Research. 11(4):614-625 where it was shown in a controlled experiment to be effective at reducing finishing labor costs) and has been distributed and supported since 1999 as part of the phred/phrap/consed software package (see, which currently has several thousand academic and commercial users.

The unnamed program you mention as reducing finishing staff workload by 75 to 80 percent at the Washington University Genome Sequencing Center is in fact Autofinish. It was not invented at Washington University in St. Louis, but rather here at the University of Washington in Seattle.

Moreover, Autofinish is in use at several of the other centers mentioned in your article, such as Stanford’s Human Genome Center. Many of your readers are aware of Autofinish and were no doubt puzzled by its omission from your article.

David Gordon
Department of Genome Sciences
University of Washington

…But the Autofinish Story Isn’t Finished

I agree with the sentiments that David Gordon expressed in his letter, but I am concerned that your readers may get the impression that I failed to properly recognize Autofinish.

In my discussion with GT senior editor John MacNeil, I am quite sure that I credited Autofinish and its authors, and mentioned that it was one of our primary prefinishing tools. In fact, we played a major role in helping David develop the program. I think some of the confusion may stem from your explanation of our process, where it reads as if Autofinish and prefinishing are the same process, where in reality, Autofinish is just one component of prefinishing.

Prefinishing at Washington University has existed since the mid-’90s at our center, and Autofinish was not incorporated into the process until 1999. Autofinish has been a tremendous enhancement to our process.

Thank you for your informative article on a very pertinent topic.

Robert Fulton
Finishing Group Leader
Genome Sequencing Center
Washington University

Cheers to IT Guy

I believe this is the second time I am writing to compliment an article featured in your magazine. Nat Goodman’s point on the downside of microarrays featured in your April issue (“Microarrays: Hazardous to Your Science”) is timely and right on target. As the co-inventor of Differential Display, a competing technology of microarrays, I am fully aware of the problems of microarrays and chose to be silent on it for obvious reasons. I started to break my silence recently, like many other leaders in the field, including Sydney Brenner.

I want to thank you for taking an objective stance in covering a technology, and not being swayed by ad money from such a technology. Many leading journals, including Science and Nature, contributed greatly to the “feeding frenzy” of microarray fever, which is finally dying down.

Keep up with your good effort and well-edited journal.

Peng Liang, PhD
Associate Professor
Vanderbilt-Ingram Cancer Center

Send us your thoughts

Send e-mail to [email protected] or mail to: Editor, Genome Technology, PO Box 998, New York, NY 10272-0998


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