Documentation for LIAN 3 . 5 Bernhard Haubold
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چکیده
منابع مشابه
andi: Fast and accurate estimation of evolutionary distances between closely related genomes
MOTIVATION A standard approach to classifying sets of genomes is to calculate their pairwise distances. This is difficult for large samples. We have therefore developed an algorithm for rapidly computing the evolutionary distances between closely related genomes. RESULTS Our distance measure is based on ungapped local alignments that we anchor through pairs of maximal unique matches of a mini...
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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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MOTIVATION In many organisms, including humans, recombination clusters within recombination hotspots. The standard method for de novo detection of recombinants at hotspots is sperm typing. This relies on allele-specific PCR at single nucleotide polymorphisms. Designing allele-specific primers by hand is time-consuming. We have therefore written a package to support hotspot detection and analysi...
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Special Edition “2015 UN/Japan Workshop on Space Weather” 157 Pathway Model and Nonextensive Statistical Mechanics A.M. Mathai, H.J. Haubold , C. Tsallis 5 1 Department of Mathematics and Statistics, McGill University, Quebec, Canada 2 Centre for Mathematical and Statistical Sciences, Kerala, India 3 Office for Outer Space Affairs, United Nations, Vienna, Austria 4 Centro Brasileiro de Pesquisa...
متن کاملAlignment-free detection of local similarity among viral and bacterial genomes
MOTIVATION Bacterial and viral genomes are often affected by horizontal gene transfer observable as abrupt switching in local homology. In addition to the resulting mosaic genome structure, they frequently contain regions not found in close relatives, which may play a role in virulence mechanisms. Due to this connection to medical microbiology, there are numerous methods available to detect hor...
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