8978080

Source:http://linkedlifedata.com/resource/pubmed/id/8978080

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Predicate	Object
rdf:type	pubmed:Citation
lifeskim:mentions	umls-concept:C0017337, umls-concept:C0035541, umls-concept:C0449774, umls-concept:C0596311, umls-concept:C1330957, umls-concept:C1881865
pubmed:issue	4
pubmed:dateCreated	1997-3-31
pubmed:abstractText	We propose a simple algorithm for estimating the number of nucleotide differences between a pair of RNA or DNA sequences through comparison of their RNAse A mismatch cleavage patterns. In the RNAse A mismatch cleavage technique two or more sample sequences are hybridized to the same RNA probe, the hybrids are partially digested with RNAse A, and the digestion products are compared on an electrophoretic gel. Here we provide an algorithm for converting the numbers of unique and matching electrophoretic bands into an estimate of the number of nucleotide differences between the sequences. Computer simulation indicates that the proposed method yields a robust estimate of the genetic distance despite stochastic errors and occasional violation of certain assumptions. Our study suggests that the method performs best when the distance between the sequences is < 15 differences. When the sequences under analysis are likely to have larger distances, we advise to substitute one long riboprobe with a set of shorter nonoverlapping probes. The new algorithm is applied to infer the proximity of several strains of pseudorabies virus.
pubmed:commentsCorrections	http://linkedlifedata.com/resource/pubmed/commentcorrection/8978080-1482122, http://linkedlifedata.com/resource/pubmed/commentcorrection/8978080-2034672, http://linkedlifedata.com/resource/pubmed/commentcorrection/8978080-2415964, http://linkedlifedata.com/resource/pubmed/commentcorrection/8978080-2438556, http://linkedlifedata.com/resource/pubmed/commentcorrection/8978080-265521, http://linkedlifedata.com/resource/pubmed/commentcorrection/8978080-291943, http://linkedlifedata.com/resource/pubmed/commentcorrection/8978080-3176343, http://linkedlifedata.com/resource/pubmed/commentcorrection/8978080-3368463, http://linkedlifedata.com/resource/pubmed/commentcorrection/8978080-4071043, http://linkedlifedata.com/resource/pubmed/commentcorrection/8978080-7063400, http://linkedlifedata.com/resource/pubmed/commentcorrection/8978080-7762293, http://linkedlifedata.com/resource/pubmed/commentcorrection/8978080-8270657, http://linkedlifedata.com/resource/pubmed/commentcorrection/8978080-8837888
pubmed:language	eng
pubmed:journal	http://linkedlifedata.com/resource/pubmed/journal/0374636
pubmed:citationSubset	IM
pubmed:chemical	http://linkedlifedata.com/resource/pubmed/chemical/DNA, http://linkedlifedata.com/resource/pubmed/chemical/RNA
pubmed:status	MEDLINE
pubmed:month	Dec
pubmed:issn	0016-6731
pubmed:author	pubmed-author:AyalaF JFJ, pubmed-author:DanglerC ACA, pubmed-author:DopazoJJ, pubmed-author:RzhetskyAA, pubmed-author:SnyderEE
pubmed:issnType	Print
pubmed:volume	144
pubmed:owner	NLM
pubmed:authorsComplete	Y
pubmed:pagination	1975-83
pubmed:dateRevised	2009-11-18
pubmed:meshHeading	pubmed-meshheading:8978080-Algorithms, pubmed-meshheading:8978080-Animals, pubmed-meshheading:8978080-DNA, pubmed-meshheading:8978080-Genes, pubmed-meshheading:8978080-Humans, pubmed-meshheading:8978080-RNA, pubmed-meshheading:8978080-Sequence Analysis
pubmed:year	1996
pubmed:articleTitle	Assessing dissimilarity of genes by comparing their RNAse A mismatch cleavage patterns.
pubmed:affiliation	Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park 16802, USA. andrey@genome2.cpmc.columbia.edu
pubmed:publicationType	Journal Article, Research Support, U.S. Gov't, P.H.S., Research Support, U.S. Gov't, Non-P.H.S.