Detecting lateral genetic material transfer

The bioinformatical methods to detect lateral gene transfer events are mainly based on functional coding DNA characteristics. In this paper, we propose the use of DNA traits not depending on protein coding requirements. We introduce several semilocal variables that depend on DNA primary sequence and that reflect thermodynamic as well as physico-chemical magnitudes that are able to tell apart the genome of different organisms. After combining these variables in a neural classificator, we obtain results whose power of resolution go as far as to detect the exchange of genomic material between bacteria that are phylogenetically close.

[1]  M. Tomita,et al.  CpG distribution patterns in methylated and non-methylated species. , 1997, Gene.

[2]  S Karlin,et al.  Detecting Alien Genes in Bacterial Genomes a , 1999, Annals of the New York Academy of Sciences.

[3]  Cathy H. Wu.  Artificial Neural Networks for Molecular Sequence Analysis , 1997, Comput. Chem..

[4]  Eugen C. Buehler,et al.  Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana , 1999, Nature.

[5]  Sean D. Hooper,et al.  Detection of Genes with Atypical Nucleotide Sequence in Microbial Genomes , 2002, Journal of Molecular Evolution.

[6]  Sanjeev S. Tambe,et al.  ANN Modeling of DNA Sequences: New Strategies using DNA Shape Code , 2000, Comput. Chem..

[7]  J. Eisen.  Horizontal gene transfer among microbial genomes: new insights from complete genome analysis. , 2000, Current opinion in genetics & development.

[8]  Björn Olsson,et al.  Artificial intelligence techniques for bioinformatics. , 2002, Applied bioinformatics.

[9]  C. Tupper.  Horizontal gene transfer and phylogenetics HervePhilippeand Christophe J Douady y , 2003 .

[10]  A. Brennicke,et al.  The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides , 1997, Nature Genetics.

[11]  C. Kurland,et al.  Horizontal gene transfer: A critical view , 2003 .

[12]  H. Ochman,et al.  Amelioration of Bacterial Genomes: Rates of Change and Exchange , 1997, Journal of Molecular Evolution.

[13]  Yong Wang,et al.  Cytosine Methylation Is Not the Major Factor Inducing CpG Dinucleotide Deficiency in Bacterial Genomes , 2004, Journal of Molecular Evolution.

[14]  Alessandra Carbone,et al.  Codon adaptation index as a measure of dominating codon bias , 2003, Bioinform..

[15]  I Mahadevan,et al.  Analysis of E.coli promoter structures using neural networks. , 1994, Nucleic acids research.

[16]  R. Dickerson,et al.  Structure of a B-DNA decamer with a central T-A step: C-G-A-T-T-A-A-T-C-G. , 1992, Journal of molecular biology.

[17]  Olga Zhaxybayeva,et al.  Genome mosaicism and organismal lineages. , 2004, Trends in genetics : TIG.

[18]  E. Uberbacher,et al.  Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[19]  R. Cedergren,et al.  Structural and thermodynamic properties of DNA uncover different evolutionary histories , 2004, Journal of Molecular Evolution.

[20]  P. Langford,et al.  Natural genetic exchange between Haemophilus and Neisseria: intergeneric transfer of chromosomal genes between major human pathogens. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[21]  M. Ragan.  Detection of lateral gene transfer among microbial genomes. , 2001, Current opinion in genetics & development.

[22]  L. Orgel,et al.  Phylogenetic Classification and the Universal Tree , 1999 .