Estimating the repeat structure and length of DNA sequences using L-tuples.
In shotgun sequencing projects, the genome or BAC length is not always known. We approach estimating genome length by first estimating the repeat structure of the genome or BAC, sometimes of interest in its own right, on the basis of a set of random reads from a genome project. Moreover, we can find the consensus for repeat families before assembly. Our methods are based on the l-tuple content of the reads.
Li
Xiaoman
X
Department of Mathematics, University of Southern California, Los Angeles, California 90089, USA. xiaomanl@yahoo.com
Waterman
Michael S
MS
D000465:Algorithms; D001482:Base Composition; D002874:Chromosome Mapping / Q000706:statistics & numerical data; D022202:Chromosomes, Artificial, Bacterial; D019295:Computational Biology / Q000706:statistics & numerical data; D003198:Computer Simulation / Q000706:statistics & numerical data; D016384:Consensus Sequence; D004269:DNA, Bacterial / Q000235:genetics*; D008432:Mathematical Computing; D016012:Poisson Distribution; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D012984:Software
D004269:DNA, Bacterial