Software systems for a DNA sequencer

• Main Author: Ait-Ghezala, Ahmed, 1976-
• Other Authors: Paul Matsudaira.
• Format: Others
• Language: English
• Published: Massachusetts Institute of Technology 2005
• Subjects: Electrical Engineering and Computer Science.
• Online Access: http://hdl.handle.net/1721.1/8931

Thesis (M.Eng. and S.B.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2000. === Includes bibliographical references (leaf 49). === The initiative to complete the sequencing of the human genome is bringing the need for high-throughput sequencing capabilities to the forefront. We at the BioMEMS engineering group at the Whitehead Institute are designing and building a new sequencing machine that uses a 384 glass "chip" to dramatically increase sequencing rates. This thesis describes the design and implementation of two of the machine's software components. The first is a prototype application for the control of a robot used to automate sample loading. The second is a software filter that allows us to generate quality scores from data processed by Trout using Phred. I present the algorithm used to perform the filtering and show that the results are comparable to the processing of data with the Plan- Phred processing package. === by Ahmed Ait-Ghezala. === M.Eng.and S.B.