De novo repeat classification and fragment assembly

被引：142

作者：

Pevzner, PA

Tang, HX

Tesler, G ^{[1
]}

机构：

[1] Univ Calif San Diego, Dept Math, La Jolla, CA 92093 USA

[2] Univ Calif San Diego, Dept Comp Sci & Engn, La Jolla, CA 92093 USA

来源：

GENOME RESEARCH | 2004年 / 14卷 / 09期

关键词：

D O I：

10.1101/gr.2395204

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Repetitive sequences make up a significant fraction of almost any genome, and an important and still open question in bioinformatics is how to represent all repeats in DNA sequences. We propose a new approach to repeat classification that represents all repeats in a genome as a mosaic of sub-repeats. Our key algorithmic idea also leads to new approaches to multiple alignment and fragment assembly. In particular, we show that our FragmentGluer assembler improves on Phrap and ARACHNE in assembly of BACs and bacterial genomes.

引用

页码：1786 / 1796

页数：11

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