منابع مشابه
An alignment-free test for recombination
MOTIVATION Why recombination? is one of the central questions in biology. This has led to a host of methods for quantifying recombination from sequence data. These methods are usually based on aligned DNA sequences. Here, we propose an efficient alignment-free alternative. RESULTS Our method is based on the distribution of match lengths, which we look up using enhanced suffix arrays. By elimi...
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In this paper, we study a new version of multiple sequence alignment, xed topology alignment with recombination. We show that it can not be approximated within any constant ratio unless P = NP. For a more restricted version, we show that the problem is MAX-SNP-hard. This implies that there is no PTAS for this version unless P = NP. We also propose approximation algorithms for a special case, wh...
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MOTIVATION Some recent comparative studies have revealed that regulatory regions can retain function over large evolutionary distances, even though the DNA sequences are divergent and difficult to align. It is also known that such enhancers can drive very similar expression patterns. This poses a challenge for the in silico detection of biologically related sequences, as they can only be discov...
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Phylogeny reconstruction on a genome scale remains computationally challenging even for closely related organisms. Here we propose an alignmentfree pairwise distance measure, Kr, for genomes separated by less than approximately 0.5 mismatches/nucleotide. We have implemented the computation of Kr based on enhanced suffix arrays in the program kr, which is freely available from guanine.evolbio.mp...
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We introduce the first polynomial-time phylogenetic reconstruction algorithm under a model of sequence evolution allowing insertions and deletions—or indels. Given appropriate assumptions, our algorithm requires sequence lengths growing polynomially in the number of leaf taxa. Our techniques are distance-based and largely bypass the problem of multiple alignment. ∗CSAIL, MIT. †Department of Mat...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2013
ISSN: 1460-2059,1367-4803
DOI: 10.1093/bioinformatics/btt550