<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Martin, M. J.</style></author><author><style face="normal" font="default" size="100%">Herrero, J.</style></author><author><style face="normal" font="default" size="100%">A. Mateos</style></author><author><style face="normal" font="default" size="100%">Dopazo, J.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Comparing bacterial genomes through conservation profiles</style></title><secondary-title><style face="normal" font="default" size="100%">Genome Res</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Bacterial Genotype Models</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial/genetics Cluster Analysis Conserved Sequence/*genetics DNA</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial/genetics Escherichia coli/classification/*genetics Evolution</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial/genetics Gene Order/genetics Genes</style></keyword><keyword><style  face="normal" font="default" size="100%">Bacterial/genetics/physiology *Genome</style></keyword><keyword><style  face="normal" font="default" size="100%">Chromosome Mapping/methods Chromosomes</style></keyword><keyword><style  face="normal" font="default" size="100%">Genetic Phenotype Phylogeny Sequence Homology</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Gene Expression Profiling/methods Gene Expression Regulation</style></keyword><keyword><style  face="normal" font="default" size="100%">Nucleic Acid Species Specificity Terminology as Topic</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2003</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=12695324</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">5</style></number><volume><style face="normal" font="default" size="100%">13</style></volume><pages><style face="normal" font="default" size="100%">991-8</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">We constructed two-dimensional representations of profiles of gene conservation across different genomes using the genome of Escherichia coli as a model. These profiles permit both the visualization at the genome level of different traits in the organism studied and, at the same time, reveal features related to the genomes analyzed (such as defective genomes or genomes that lack a particular system). Conserved genes are not uniformly distributed along the E. coli genome but tend to cluster together. The study of gene distribution patterns across genomes is important for the understanding of how sets of genes seem to be dependent on each other, probably having some functional link. This provides additional evidence that can be used for the elucidation of the function of unannotated genes. Clustering these patterns produces families of genes which can be arranged in a hierarchy of closeness. In this way, functions can be defined at different levels of generality depending on the level of the hierarchy that is studied. The combined study of conservation and phenotypic traits opens up the possibility of defining phenotype/genotype associations, and ultimately inferring the gene or genes responsible for a particular trait.</style></abstract><notes><style face="normal" font="default" size="100%">Martin, Maria J Herrero, Javier Mateos, Alvaro Dopazo, Joaquin Comparative Study United States Genome research Genome Res. 2003 May;13(5):991-8. Epub 2003 Apr 14.</style></notes></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Nunez, J. I.</style></author><author><style face="normal" font="default" size="100%">Martin, M. J.</style></author><author><style face="normal" font="default" size="100%">Piccone, M. E.</style></author><author><style face="normal" font="default" size="100%">Carrillo, E.</style></author><author><style face="normal" font="default" size="100%">Palma, E. L.</style></author><author><style face="normal" font="default" size="100%">Dopazo, J.</style></author><author><style face="normal" font="default" size="100%">Sobrino, F.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Identification of optimal regions for phylogenetic studies on VP1 gene of foot-and-mouth disease virus: analysis of types A and O Argentinean viruses</style></title><secondary-title><style face="normal" font="default" size="100%">Vet Res</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Amino Acid Sequence Animals Aphthovirus/classification/*genetics Base Sequence Capsid/chemistry/*genetics Capsid Proteins DNA</style></keyword><keyword><style  face="normal" font="default" size="100%">Complementary/chemistry Molecular Sequence Data *Phylogeny Polymerase Chain Reaction RNA</style></keyword><keyword><style  face="normal" font="default" size="100%">Viral/chemistry/genetics Serotyping Viral Proteins/analysis/*genetics</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2001</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=11254175</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">1</style></number><volume><style face="normal" font="default" size="100%">32</style></volume><pages><style face="normal" font="default" size="100%">31-45</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">An analysis of the informative content of sequence stretches on the foot-and-mouth disease virus (FMDV) VPI gene was applied to two important viral serotypes: A and O. Several sequence regions were identified to allow the reconstruction of phylogenetic trees equivalent to those derived from the whole VPI gene. The optimal informative regions for sequence windows of 150 to 250 nt were predicted between positions 250 and 550 of the gene. The sequences spanning the 250 nt of the 3’ end (positions 400 to 650), extensively used for FMDV phylogenetic analyses, showed a lower informative content. In spite of this, the use of sequences from this region allowed the derivation of phylogenetic trees for type A and type O FMDVs which showed topologies similar to those previously reported for the whole VP1 gene. When the sequences determined for viruses isolated in Argentina, between 1990 and 1993, were included in these analyses, the results obtained revealed features of the circulation of type A and type O viruses in the field, in the months that preceded the eradication of the disease in this country. Type A viruses were closely related to an Argentinean vaccine strain, and defined an independent cluster within this serotype. Among the type O viruses analysed, two groups were distinguished; one was closely related to the South American vaccine strains, while the other was grouped with viruses of the O3 subtype. In addition, a detailed phylogeny for type A FMDV is presented.</style></abstract><notes><style face="normal" font="default" size="100%">Nunez, J I Martin, M J Piccone, M E Carrillo, E Palma, E L Dopazo, J Sobrino, F Research Support, Non-U.S. Gov’t France Veterinary research Vet Res. 2001 Jan-Feb;32(1):31-45.</style></notes></record></records></xml>