Software systems for a DNA sequencer

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.

Department dc:contributor.department

Massachusetts Institute of Technology. Dept. of Electrical Engineering and Computer Science.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2000

Author dc:creator

• Ait-Ghezala, Ahmed, 1976-

Advisor dc:contributor.advisor

• Paul Matsudaira.

• Electrical Engineering and Computer Science.

Statement dc:rights

• M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/8931

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/8931