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An Efficient Algorithm for the Identification of Structured Motifs in DNA Promoter Sequences
April-June 2006 (vol. 3 no. 2)
pp. 126-140
ASCII Text
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Alexandra M. Carvalho, Ana T. Freitas, Arlindo L. Oliveira, Marie-France Sagot, "An Efficient Algorithm for the Identification of Structured Motifs in DNA Promoter Sequences," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 3, no. 2, pp. 126-140, April-June, 2006.
 
 
BibTex
x
 
@article{ 10.1109/TCBB.2006.16,
author = {Alexandra M. Carvalho and Ana T. Freitas and Arlindo L. Oliveira and Marie-France Sagot},
title = {An Efficient Algorithm for the Identification of Structured Motifs in DNA Promoter Sequences},
journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
volume = {3},
number = {2},
issn = {1545-5963},
year = {2006},
pages = {126-140},
doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2006.16},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
x 
 
TY - JOUR
JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics
TI - An Efficient Algorithm for the Identification of Structured Motifs in DNA Promoter Sequences
IS - 2
SN - 1545-5963
SP126
EP140
EPD - 126-140
A1 - Alexandra M. Carvalho,
A1 - Ana T. Freitas,
A1 - Arlindo L. Oliveira,
A1 - Marie-France Sagot,
PY - 2006
KW - Box-link
KW - factor tree
KW - structured motif
KW - promoter
KW - binding site consensus.
VL - 3
JA - IEEE/ACM Transactions on Computational Biology and Bioinformatics
ER -
 
We propose a new algorithm for identifying cis-regulatory modules in genomic sequences. The proposed algorithm, named RISO, uses a new data structure, called box-link, to store the information about conserved regions that occur in a well-ordered and regularly spaced manner in the data set sequences. This type of conserved regions, called structured motifs, is extremely relevant in the research of gene regulatory mechanisms since it can effectively represent promoter models. The complexity analysis shows a time and space gain over the best known exact algorithms that is exponential in the spacings between binding sites. A full implementation of the algorithm was developed and made available online. Experimental results show that the algorithm is much faster than existing ones, sometimes by more than four orders of magnitude. The application of the method to biological data sets shows its ability to extract relevant consensi.

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Index Terms:
Box-link, factor tree, structured motif, promoter, binding site consensus.
Citation:
Alexandra M. Carvalho, Ana T. Freitas, Arlindo L. Oliveira, Marie-France Sagot, "An Efficient Algorithm for the Identification of Structured Motifs in DNA Promoter Sequences," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 3, no. 2, pp. 126-140, April-June 2006, doi:10.1109/TCBB.2006.16
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