Optimistically building a consensus sequence using ℱ-inexact matches [DNA]

Author

Cull, P. ; Holloway, J.L.

Author_Institution

Dept. of Comput. Sci., Oregon State Univ., Corvallis, OR, USA

Volume

i

fYear

1992

fDate

7-10 Jan 1992

Firstpage

643

Abstract

Biological and physical limitations require that DNA be sequenced in fragments. During the process of sequencing the DNA, errors are occasionally introduced. This paper addresses the problem of reconstructing the original DNA sequence given only the fragments that may contain errors. The authors give a new algorithm based on suffix arrays to solve the problem of reconstructing the original DNA sequence. A worst-case and expected-case time analysis of the algorithm is presented. A program based on this algorithm is used to reconstruct the human beta globin region on chromosome 11 (HUMHBB in GenBank) when given a set of 300 to 500 mers drawn randomly from the HUMHBB locus

Keywords

DNA; biology computing; errors; DNA sequence; F-inexact matches; GenBank; HUMHBB locus; chromosome 11; errors; fragments; human beta globin; optimistic consensus sequence reconstruction; suffix arrays; Assembly; Biological cells; Biology; Computer errors; Computer science; DNA; Humans; Lead; RNA; Sequences;

fLanguage

English

Publisher

ieee

Conference_Titel

System Sciences, 1992. Proceedings of the Twenty-Fifth Hawaii International Conference on

Conference_Location

Kauai, HI

Print_ISBN

0-8186-2420-5

Type

conf

DOI

10.1109/HICSS.1992.183217

Filename

183217