SUNNYVALE, Calif.--Amersham Pharmacia Biotech, the life sciences division of Nycomed Amersham, announced that the new version of Phred, the sequencing analysis program used by high-throughput DNA sequencing facilities, has been recalibrated for data produced by its MegaBace 1000 DNA sequencer. So far, it is the only capillary sequencer to be validated with the new Phred version, which is being released by the University of Washington.
MegaBace 1000 was officially introduced this month at the Sixth International Automation in Mapping and DNA Sequencing Conference in Cambridge, UK. "We originally developed Phred for use with older, fluorescent slab gel systems. The data produced by capillary sequencers required a refinement to the program and validation to ensure agreement between predicted quality values and actual quality values in Phred," said Brent Ewing of the University of Washington's molecular biotechnology department. "We have verified that the quality values assigned by Phred are accurate for data produced by MegaBace, and we used over four million base pairs of data supplied by the genome community to calibrate Phred for it."
Ewing has also worked with Amersham Pharmacia to enable the latest Phred version to accept the MegaBace file format directly, making the data analysis process more efficient. The new version will be available as an update to existing Phred users this month.