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The repetitive structure of genomic DNA holds many secrets to be discovered. A systematic study of repetitive DNA on a genomic or inter-genomic scale requires extensive algorithmic support. The REPuter program described herein was designed to serve as a fundamental tool in such studies. Efficient and complete detection of various types of repeats is(More)
MOTIVATION We present a new probabilistic model of the evolution of RNA-, DNA-, or protein-like sequences and a software tool, Rose, that implements this model. Guided by an evolutionary tree, a family of related sequences is created from a common ancestor sequence by insertion, deletion and substitution of characters. During this artificial evolutionary(More)
We present an efficient implementation of a write-only topdown construction for suffix trees. Our implementation is based on a new, space-efficient representation of suffix trees which requires only 12 bytes per input character in the worst case, and 8.5 bytes per input character on average for a collection of files of different type. We show how to(More)
Metagenomics is providing striking insights into the ecology of microbial communities. The recently developed massively parallel 454 pyrosequencing technique gives the opportunity to rapidly obtain metagenomic sequences at a low cost and without cloning bias. However, the phylogenetic analysis of the short reads produced represents a significant(More)
We study the problem of detecting all occurrences of (primitive) tandem repeats and tandem arrays in a string. We first give a simple timeand space-optimal algorithm to find all tandem repeats, and then modify it to become a time and space-optimal algorithm for finding only the primitive tandem repeats. Both of these algorithms are then extended to handle(More)
The vast majority of microbes are unculturable and thus cannot be sequenced by means of traditional methods. High-throughput sequencing techniques like 454 or Solexa-Illumina make it possible to explore those microbes by studying whole natural microbial communities and analysing their biological diversity as well as the underlying metabolic pathways. Over(More)
Numerous tools have been developed to align genomic sequences. However, their relative performance in specific applications remains poorly characterized. Alignments of protein-coding sequences typically have been benchmarked against "correct" alignments inferred from structural data. For noncoding sequences, where such independent validation is lacking,(More)
The study of genome rearrangements is an important tool in comparative genomics. This paper revisits the problem of sorting a multichromosomal genome by translocations, i.e., exchanges of chromosome ends. We give an elementary proof of the formula for computing the translocation distance in linear time, and we give a new algorithm for sorting by(More)