De novo repeat classification and fragment assembly.

by: PA Pevzner, H Tang, G Tesler

Genome Res, Vol. 14, No. 9. (September 2004), pp. 1786-1796.

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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.

@article{citeulike:79831, abstract = {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.}, address = {Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92093, USA.}, author = {Pevzner, P. A. and Tang, H. and Tesler, G. }, citeulike-article-id = {79831}, doi = {10.1101/gr.2395204}, issn = {1088-9051}, journal = {Genome Res}, keywords = {clustering, graph, repeatgluer, te}, month = {September}, number = {9}, pages = {1786--1796}, posted-at = {2008-01-17 12:51:04}, priority = {1}, title = {De novo repeat classification and fragment assembly.}, url = {http://dx.doi.org/10.1101/gr.2395204}, volume = {14}, year = {2004} }

RIS record

TY - JOUR ID - citeulike:79831 L3 - citeulike-article-id:79831 TI - De novo repeat classification and fragment assembly. JF - Genome Res VL - 14 IS - 9 SP - 1786 EP - 1796 AD - Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92093, USA. SN - 1088-9051 N2 - 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. KW - clustering KW - graph KW - repeatgluer KW - te AU - Pevzner, PA AU - Tang, H AU - Tesler, G PY - 2004/09// UR - http://dx.doi.org/10.1101/gr.2395204 ER -

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