caa a22 4500 445842539 CHVBK 20180317145349.0 cr unu---uuuuu 170323e20110301xx s 000 0 eng 10.1007/s11047-010-9232-y doi (NATIONALLICENCE)springer-10.1007/s11047-010-9232-y DNA chips for species identification and biological phylogenies [Elektronische Daten] [Max Garzon, Tit-Yee Wong] The codeword design problem is an important problem in DNA computing and its applications. Several theoretical analyses as well as practical solutions for short oligonucleotides (up to 20-mers) have been generated recently. These solutions have, in turn, suggested new applications to DNA-based indexing and natural language processing, in addition to the obvious applications to the problems of reliability and scalability that generated them. Here we continue the exploration of this type of DNA-based indexing for biological applications and show that DNA noncrosshybridizing (nxh) sets can be successfully applied to infer ab initio phylogenetic trees by providing a way to measure distances among different genomes indexed by sets of short oligonucleotides selected so as to minimize crosshybridization. These phylogenies are solidly established and well accepted in biology. The new technique is much more effective in terms of signal-to-noise ratio, cost and time than current methods. Second, it is demonstrated that DNA indexing does provide novel and principled insights into the phylogenesis of organisms hitherto inaccessible by current methods, such as a prediction of the origin of the Salmonella plasmid 50 as being acquired horizontally, likely from some bacteria somewhat related to Yesinia. Finally, DNA indexing can be scaled up to newly available universal DNA chips readily available both in vitro and in silico. In particular, we show how a recently obtained such set of nxh 16-mers can be used as a universal coordinate system in DNA spaces to characterize very large groups (families, genera, and even phylla) of organisms on a uniform biomarker reference system, a veritable and comprehensive "Atlas of Life”, as it is or as it could be on earth. Springer Science+Business Media B.V., 2010 DNA codeword design nationallicence Noncrosshybridizing oligonucleotide bases nationallicence Phylogenetic analysis nationallicence Genomic signatures nationallicence DNA chips nationallicence 16S rRNA tree of life nationallicence Garzon Max Department of Computer Science, The University of Memphis, 38152, Memphis, TN, USA aut Wong Tit-Yee Department of Biology, The University of Memphis, 38152, Memphis, TN, USA aut Natural Computing Springer Netherlands 10/1(2011-03-01), 375-389 1567-7818 10:1<375 2011 10 11047 https://doi.org/10.1007/s11047-010-9232-y text/html Onlinezugriff via DOI 1 research-article jats NATIONALLICENCE 856 40 https://doi.org/10.1007/s11047-010-9232-y text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Garzon Max Department of Computer Science, The University of Memphis, 38152, Memphis, TN, USA aut NATIONALLICENCE 700 1- Wong Tit-Yee Department of Biology, The University of Memphis, 38152, Memphis, TN, USA aut NATIONALLICENCE 773 0- Natural Computing Springer Netherlands 10/1(2011-03-01), 375-389 1567-7818 10:1<375 2011 10 11047 Metadata rights reserved Springer special CC-BY-NC licence nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-springer