Literature DB >> 10977084

Computation and visualization of degenerate repeats in complete genomes.

S Kurtz1, E Ohlebusch, C Schleiermacher, J Stoye, R Giegerich.   

Abstract

The repetitive structure of genomic DNA holds many secrets to be discovered. A systematic study of repetitive DNA on a genomic or inter-genomic scale requires extensive algorithmic support. The REPuter family of programs described herein was designed to serve as a fundamental tool in such studies. Efficient and complete detection of various types of repeats is provided together with an evaluation of significance, interactive visualization, and simple interfacing to other analysis programs.

Mesh:

Year:  2000        PMID: 10977084

Source DB:  PubMed          Journal:  Proc Int Conf Intell Syst Mol Biol        ISSN: 1553-0833


  8 in total

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2.  De novo repeat classification and fragment assembly.

Authors:  Pavel A Pevzner; Paul A Pevzner; Haixu Tang; Glenn Tesler
Journal:  Genome Res       Date:  2004-09       Impact factor: 9.043

3.  Identification of transposable elements using multiple alignments of related genomes.

Authors:  Anat Caspi; Lior Pachter
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4.  Skittle: a 2-dimensional genome visualization tool.

Authors:  Josiah D Seaman; John C Sanford
Journal:  BMC Bioinformatics       Date:  2009-12-30       Impact factor: 3.169

5.  Genome sequencing and analysis of Yersina pestis KIM D27, an avirulent strain exempt from select agent regulation.

Authors:  Liliana Losada; John J Varga; Jessica Hostetler; Diana Radune; Maria Kim; Scott Durkin; Olaf Schneewind; William C Nierman
Journal:  PLoS One       Date:  2011-04-29       Impact factor: 3.240

6.  A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes.

Authors:  Daniel H Haft; Jeremy Selengut; Emmanuel F Mongodin; Karen E Nelson
Journal:  PLoS Comput Biol       Date:  2005-11-11       Impact factor: 4.475

7.  Insertion Sequences show diverse recent activities in Cyanobacteria and Archaea.

Authors:  Fengfeng Zhou; Victor Olman; Ying Xu
Journal:  BMC Genomics       Date:  2008-01-24       Impact factor: 3.969

8.  CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats.

Authors:  Ibtissem Grissa; Gilles Vergnaud; Christine Pourcel
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  8 in total

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