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  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, Troy University, Troy, AL 36082, USA




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