'Genomemark': detecting word periodicity in biological sequences.
Identifying and predicting the structural characteristics of novel repeats throughout the genome can lend insight into biological function. Specific repeats are believed to have biological significance as a function of their distribution patterns. We have developed 'GenomeMark,' a computer program that detects and statistically analyzes candidate repeats. Specifically, 'GenomeMark' identifies the periodic distribution of unique words, calculating their chi2 and Z-score values. Using 'GenomeMark,' we identified novel sequence words present in tandem throughout genomes. We found that these sequences have remarkable spacer sequence distributions and many were genome specific, validating the genome signature theory. Further analysis confirmed that many of these sequences have a specific biological function. The program is available from the authors upon request and is freely available for non-commercial and academic entities.
Fadiel
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Yale University School of Medicine, Yale Center for Research On Reproductive Biology, New Haven, CT 06511, USA. afadiel@yale.edu
Eichenbaum
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Hamza
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D000465:Algorithms; D001105:Archaea / Q000235:genetics; D001419:Bacteria / Q000235:genetics; D023281:Genomics / Q000706:statistics & numerical data; D008390:Markov Chains; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA / Q000706:statistics & numerical data; D012984:Software