02356nas a2200265   4500008004100000245006200041210006200103300001000165490000700175520124200182653003001424653007301454653007501527653004901602653004201651653004301693653005001736653007501786653005801861100001901919700001601938700001501954700001501969856010601984       2003                        eng d00aComparing bacterial genomes through conservation profiles0 aComparing bacterial genomes through conservation profiles  a991-80 v133 aWe 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.10aBacterial Genotype Models10aBacterial/genetics Cluster Analysis Conserved Sequence/*genetics DNA10aBacterial/genetics Escherichia coli/classification/*genetics Evolution10aBacterial/genetics Gene Order/genetics Genes10aBacterial/genetics/physiology *Genome10aChromosome Mapping/methods Chromosomes10aGenetic Phenotype Phylogeny Sequence Homology10aMolecular Gene Expression Profiling/methods Gene Expression Regulation10aNucleic Acid Species Specificity Terminology as Topic1 aMartin, M., J.1 aHerrero, J.1 aMateos, A.1 aDopazo, J.  uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1269532402532nas a2200229   4500008004100000245015400041210006900195300001000264490000700274520149500281653013001776653009301906653007401999100001802073700001902091700002002110700001702130700001802147700001502165700001602180856010602196       2001                        eng d00aIdentification of optimal regions for phylogenetic studies on VP1 gene of foot-and-mouth disease virus: analysis of types A and O Argentinean viruses0 aIdentification of optimal regions for phylogenetic studies on VP  a31-450 v323 aAn 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.10aAmino Acid Sequence Animals Aphthovirus/classification/*genetics Base Sequence Capsid/chemistry/*genetics Capsid Proteins DNA10aComplementary/chemistry Molecular Sequence Data *Phylogeny Polymerase Chain Reaction RNA10aViral/chemistry/genetics Serotyping Viral Proteins/analysis/*genetics1 aNunez, J., I.1 aMartin, M., J.1 aPiccone, M., E.1 aCarrillo, E.1 aPalma, E., L.1 aDopazo, J.1 aSobrino, F.  uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11254175