Project Period
July 1, 1999-June 30, 2001
Level of Access
Open-Access Report
Grant Number
9902565
Submission Date
12-11-2000
Abstract
An investigation into improving the performance of DNA base calling algorithms was conducted. The results have shown that the preprocessing steps performed by ABI sequencer on raw data adversely affects the accuracy of DNA sequencing. This adverse effect has been responsible for relatively high error rates, between 3.5% to 6%, in both ABI and Phred sequencing software. Please note that Phred also uses the processed data generated by ABI sequencer; only their base-calling algorithm is different. To remedy this effect, we have developed and implemented a new filtering technique that preserves the initial information contained in the raw data. This provides qualitatively superior data for the future base calling step. Our proposed filtering step provides mechanical shift compensation, cross-talk filtering, and baseline adjustment. These have been briefly described below. Application of our filtering step on a limited number of DNA data has provided sequences with lower error rate.
Rights and Access Note
This Item is protected by copyright and/or related rights. You are free to use this Item in any way that is permitted by the copyright and related rights legislation that applies to your use. In addition, no permission is required from the rights-holder(s) for educational uses. For other uses, you need to obtain permission from the rights-holder(s).
Recommended Citation
Musavi, Mohamad T., "An Intelligent System for Automated DNA Base Calling" (2000). University of Maine Office of Research Administration: Grant Reports. 262.
https://digitalcommons.library.umaine.edu/orsp_reports/262
Included in
Rights Statement
Additional Participants
Post-doc
Cristian Domnisoru
Graduate Student
Xiang Zhan
Organizational Partners
DNA Sequencing Core Facility at University of Maine
Other Collaborators or Contacts
Jurgan Naggert, Jackson Laboratory
Douglas McMinimy, Jackson Laboratory