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We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome.(More)
MOTIVATION Error correction is critical to the success of next-generation sequencing applications, such as resequencing and de novo genome sequencing. It is especially important for high-throughput short-read sequencing, where reads are much shorter and more abundant, and errors more frequent than in traditional Sanger sequencing. Processing massive numbers(More)
Phylogenetic inference is a <i>grand challenge</i> in Bioinformatics due to immense computational requirements. The increasing popularity of multi-gene alignments in biological studies, which typically provide a stable topological signal due to a more favorable ratio of the number of base pairs to the number of sequences, coupled with rapid accumulation of(More)
We describe a whole-genome assembly program named PCAP for processing tens of millions of reads. The PCAP program has several features to address efficiency and accuracy issues in assembly. Multiple processors are used to perform most time-consuming computations in assembly. A more sensitive method is used to avoid missing overlaps caused by sequencing(More)
We present the first space and time optimal parallel algorithm for the pairwise sequence alignment problem, a fundamental problem in computational biology. This problem can be solved sequentially in O(mn) time and O(m+n) space, where m and n are the lengths of the sequences to be aligned. The fastest known parallel space-optimal algorithm for pairwise(More)
The advent of high-throughput short read technology is revolutionizing life sciences by providing an inexpensive way to sequence genomes at high coverage. Exploiting this technology requires the development of a de novo short read assembler, which is an important open problem that is garnering significant research effort. Current methods are largely limited(More)
A genetic map is an ordering of genetic markers constructed from genetic linkage data for use in linkage studies and experimental design. While traditional methods have focused on constructing maps from a single population study, increasingly maps are generated for multiple lines and populations of the same organism. For example, in crop plants, where the(More)
Graph theoretic models for genome assembly are continually being proposed and refined. At the same time, large scale assembly projects rely on the overlap-layout-consensus assembly paradigm, in which the best pairwise alignments serve as seeds for a greedy extension of contigs. These methods, which largely rely on local information, are used despite(More)
Brassinosteroids (BRs) are important regulators for plant growth and development. BRs signal to control the activities of the BES1 and BZR1 family transcription factors. The transcriptional network through which BES1 and BZR regulate large number of target genes is mostly unknown. By combining chromatin immunoprecipitation coupled with Arabidopsis tiling(More)