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OJBTM
Online Journal of Bioinformatics©
Volume 9 (2):121-129, 2008
MOTIFA (Motif Analyzer): examination of interregional
and intraregional distribution of short DNA motifs
Sucaet Y, Magrath
C
Biological and Environmental
Science,
ABSTRACT
Sucaet Y Magrath C, MOTIFA
(Motif Analyzer): examination of interregional and intraregional distribution
of short DNA motifs, Online J Bioinformatics, 9
(2): 121-129, 2008. Analysis of short sequence motifs in specific
regions of genomes is difficult and many common applications used for motif
analysis have critical shortcomings, including a limitation on the size of the
motif and a limit on the number of hits possible. The Motif Analyzer
(MOTIFA) is designed to allow specific motifs of any length to be identified
and analyzed with no restriction on the number of hits, still allowing
potential variation in a motif. Overlapping sequences are considered in
the analysis and the output is convenient for statistical analysis and graphic
visualization, as well as export to other programs. A practical
application of MOTIFA to demonstrate the capabilities of the software was
completed by assessing the overall abundance of transcription termination
sequences in S. cerevisiae and E. coli.
KEYWORDS: motif analysis, short sequence analysis,
overlapping sequences, genome, multiple datasets
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