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CENSOR--a program for identification and elimination of repetitive elements from DNA sequences
J Jurka1, P Klonowski, V Dagman
1Linus Pauling Institute of Science and Medicine, Palo Alto, CA 94306, USA.
Computers & Chemistry
|March 1, 1996
Summary
CENSOR is a new program that identifies and removes DNA sequence fragments homologous to chosen references, particularly repetitive elements. It uses established algorithms with adjustable sensitivity for accurate sequence alignment and homology detection.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Identifying homologous DNA sequences is crucial for understanding genome structure and function.
- Repetitive elements pose challenges in sequence analysis due to their abundance and similarity.
Purpose of the Study:
- To introduce CENSOR, a program for identifying and eliminating DNA sequence fragments homologous to reference sequences.
- To provide tools for distinguishing between homologous and non-homologous sequence alignments.
Main Methods:
- CENSOR utilizes the Smith & Waterman and Wilbur & Lipman algorithms for sequence alignment.
- The program incorporates pre-set sensitivity levels based on biological and statistical criteria.
- Implementation in C/C++ within the SUN/UNIX environment.
Main Results:
- CENSOR effectively identifies and removes homologous DNA sequence fragments.
- Adjustable sensitivity levels aid in differentiating between homologous and non-homologous sequence pairs.
- The program facilitates the analysis of repetitive elements within DNA sequences.
Conclusions:
- CENSOR provides a robust computational tool for DNA sequence analysis, particularly for repetitive elements.
- Its algorithm-based approach and adjustable sensitivity enhance the accuracy of homology detection.
- The program contributes to the field of bioinformatics by offering a specialized solution for sequence elimination.