A. Mark Settles

1Lilla Römisch-Margl
1Chi-Wah Tseung
1Emily Dieter
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MOTIVATION Repeats are ubiquitous in genomes and play important roles in evolution. Transposable elements are a common kind of repeat. Transposon insertions can be nested and make the task of identifying repeats difficult. RESULTS We develop a novel iterative algorithm, called Greedier, to find repeats in a target genome given a repeat library. Greedier(More)
Plants have duplicate versions of the oxidative pentose phosphate pathway (oxPPP) enzymes with a subset localized to the chloroplast. The chloroplast oxPPP provides NADPH and pentose sugars for multiple metabolic pathways. This study identified two loss-of-function alleles of the Zea mays (maize) chloroplast-localized oxPPP enzyme 6-phosphogluconate(More)
Positional cloning in maize (Zea mays) requires development of markers in the region of interest. We found that primers designed to amplify annotated insertion-deletion polymorphisms of seven base pairs or greater between B73 and Mo17 produce polymorphic markers at a 97% frequency with 49% of the products showing co-dominant fragment length polymorphisms.(More)
Growing sequencing and assembly efforts have been met by the advances in high throughput machines. However, the presence of massive amounts of repeats and transposons complicates the assembly process. Given a library of possible repeats, this paper considers the problem of identifying repeats and transposons in the fragments (also called reads) generated(More)
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