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2004 IEEE Computational Systems Bioinformatics Conference (CSB'04)
RepeatAssembler: A Package for Annotation of Full-Length Repetitive DNA Sequences in Fungal Genomes
Stanford, California
August 16-August 19
ISBN: 0-7695-2194-0
ASCII Text
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Mark L. Farman, Joshua W. Gilkerson, Jerzy W. Jaromczyk, Chuck Staben, "RepeatAssembler: A Package for Annotation of Full-Length Repetitive DNA Sequences in Fungal Genomes," Computational Systems Bioinformatics Conference, International IEEE Computer Society, pp. 464-467, 2004 IEEE Computational Systems Bioinformatics Conference (CSB'04), 2004.
 
 
BibTex
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@article{ 10.1109/CSB.2004.1332461,
author = {Mark L. Farman and Joshua W. Gilkerson and Jerzy W. Jaromczyk and Chuck Staben},
title = {RepeatAssembler: A Package for Annotation of Full-Length Repetitive DNA Sequences in Fungal Genomes},
journal ={Computational Systems Bioinformatics Conference, International IEEE Computer Society},
volume = {0},
year = {2004},
isbn = {0-7695-2194-0},
pages = {464-467},
doi = {http://doi.ieeecomputersociety.org/10.1109/CSB.2004.1332461},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
x 
 
TY - CONF
JO - Computational Systems Bioinformatics Conference, International IEEE Computer Society
TI - RepeatAssembler: A Package for Annotation of Full-Length Repetitive DNA Sequences in Fungal Genomes
SN - 0-7695-2194-0
SP464
EP467
A1 - Mark L. Farman,
A1 - Joshua W. Gilkerson,
A1 - Jerzy W. Jaromczyk,
A1 - Chuck Staben,
PY - 2004
KW - null
VL - 0
JA - Computational Systems Bioinformatics Conference, International IEEE Computer Society
ER -
 
Mark L. Farman, University of Kentucky
Joshua W. Gilkerson, University of Kentucky
Jerzy W. Jaromczyk, University of Kentucky
Chuck Staben, University of Kentucky

REPEATASSEMBLER aims to automate the identification of full-length consensus sequences for repetitive DNA fragments or the genetic material that is repeated many times throughout the genome (so-called repeats). Although there are packages with similar objectives, e.g. RECON [1], none fully meets the needs of researchers in comparative genomics.

Joining short repeating elements into full-length repeats is particularly intricate and handling this task properly is both the goal and the strength of our solution. REPEATASSEMBLER analyzes as few sequences as possible to screen out all repetitive sequences. Then it builds a set of non-redundant repeats and reports the full-length consensus sequence for each element in the set.

REPEATASSEMBLER consistently delivers repetitive sequences that agree with known full-length repeats for several fungal genomes.

Citation:
Mark L. Farman, Joshua W. Gilkerson, Jerzy W. Jaromczyk, Chuck Staben, "RepeatAssembler: A Package for Annotation of Full-Length Repetitive DNA Sequences in Fungal Genomes," csb, pp.464-467, 2004 IEEE Computational Systems Bioinformatics Conference (CSB'04), 2004
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