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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, Onl J Bioinform.,
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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