CENSOR--a program for identification and elimination of repetitive elements from DNA sequences

J Jurka; P Klonowski; V Dagman; P Pelton

doi:10.1016/s0097-8485(96)80013-1

CENSOR--a program for identification and elimination of repetitive elements from DNA sequences

Comput Chem. 1996 Mar;20(1):119-21. doi: 10.1016/s0097-8485(96)80013-1.

Authors

J Jurka¹, P Klonowski, V Dagman, P Pelton

Affiliation

¹ Linus Pauling Institute of Science and Medicine, Palo Alto, CA 94306, USA.

PMID: 8867843
DOI: 10.1016/s0097-8485(96)80013-1

Abstract

CENSOR is a program designed to identify and eliminate fragments of DNA sequences homologous to any chosen reference sequences, in particular to repetitive elements. CENSOR is based on two principal algorithms of Smith & Waterman (1981) [J. Mol. Biol. 147, 195] and Wilbur & Lipman (1983) [Proc. Natl. Acad. Sci. U.S.A. 80, 726]. It includes several pre-set sensitivity levels based on both biological and statistical criteria which help to distinguish between aligned pairs of homologous and non-homologous sequences. CENSOR has been implemented in C/C + + in the SUN/UNIX environment.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Algorithms
Base Sequence
Computer Communication Networks
Computers
Databases, Factual
Molecular Sequence Data
Repetitive Sequences, Nucleic Acid / genetics*
Sequence Alignment
Sequence Analysis
Software