We would like to respond to Nat Goodman’s article, “Private Portals: Where’s the Payback?” (09.00, p.43). It is our view that the results delivered by LabOnWeb to Mr. Goodman’s single test case are, in fact, in line with LabOnWeb’s policy of providing scientifically validated and solid results.
The sequence in the test case was an artificially modified EST sequence that contained 3 percent of randomly located sequencing errors. LabOnWeb correctly identified the gene from which the sequence was taken, however the system opted not to elongate the sequence to a full gene. LabOnWeb’s policy is to minimize the number of false positive results, and a 3 percent error rate in a sequence of that length can be attributed to factors other than sequencing errors, such as homology. We contend that this decision is scientifically justified under the circumstances.
In fact, Mr. Goodman submitted a second sequence for which the correct identification was made, however he chose not to mention this result in his report. We firmly believe that LabOnWeb provides correct results in real-life situations, accounting for sequencing errors, vectors and other phenomena.
The collection of genes and transcripts that underlies LabOnWeb’s analysis is generated by the acclaimed LEADS engine. LEADS transcript predictions have been tested in hundreds of cases and verified with a success rate of over 90% in Compugen’s molecular biology laboratory, and is successfully used by our customers to yield scientifically rigorous results.
We do however accept Mr. Goodman’s criticism concerning the scientific documentation on the site. We clearly cannot reveal completely the technical details behind LEADS, however we consider extending the existing documentation to improve the clarity of the process.
Finally, we would like to mention that we do not view LabOnWeb as a “private portal,” but rather as a research engine aimed at delivering some of Compugen’s products and services over the Web to the life science community.
Following our clarification, we invite Mr. Goodman to revisit LabOnWeb, with the hope that he will join our large and continuously growing group of satisfied customers and discover that he can safely recommend our services to his readers.
Hanne Volpin, PhD,LabOnWeb Product Manager, Compugen Ltd.
So this is your new “George of Genomics.” Congratulations, it’s dynamite! I love this issue! It’s great! We do need a magazine like this! Besides the Lee Hood story, which is right on the money, I also appreciate Nat Goodman’s comment on bioinformatics dotcoms. You guys have some real insight now, although some i-bank people won’t be too happy :-).
Guyang Matthew Huang, Ph.D., Senior Scientist, Head, Molecular Biology and Bioinformatics, PPD Discovery
I really enjoyed reading Genome Technology, and I feel that it reflects the excitement that many genome biologists are experiencing. I wish everyone the best of luck and thanks for the free subscription.
John Gill, Research & Development, Team Leader, The Institute for Genomic Research
I received a copy of your new magazine yesterday and I must say it is impressive. Nice design — your company index is perfect — and the articles (as you accomplished with BioInform) are well done. Congratulations.
Mark R. Vincent, Director of Corporate Communications and Investor Relations, CuraGen Corporation.
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