Identification of foreign gene sequences by transcript filtering against the human genome

We have developed a computational subtraction approach to detect microbial causes for putative infectious diseases by filtering a set of human tissue–derived sequences against the human genome. We demonstrate the potential of this method by identifying sequences from known pathogens in established expressed–sequence tag libraries.

[1]  D. Relman,et al.  Identification of the uncultured bacillus of Whipple's disease. , 1992, The New England journal of medicine.

[2]  B. Monk,et al.  Human Papillomavirus Type 18: Association With Poor Prognosis in Early Stage Cervical Cancer , 1996 .

[3]  M. Boguski,et al.  dbEST — database for “expressed sequence tags” , 1993, Nature Genetics.

[4]  A. Kerlavage,et al.  Complementary DNA sequencing: expressed sequence tags and human genome project , 1991, Science.

[5]  S Falkow,et al.  The agent of bacillary angiomatosis. An approach to the identification of uncultured pathogens. , 1990, The New England journal of medicine.

[6]  D. Relman.  The search for unrecognized pathogens. , 1999, Science.

[7]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[8]  Lukas Wagner,et al.  A Greedy Algorithm for Aligning DNA Sequences , 2000, J. Comput. Biol..

[9]  M. Wigler,et al.  Cloning the differences between two complex genomes , 1993, Science.

[10]  H. Hausen,et al.  A new type of papillomavirus DNA, its presence in genital cancer biopsies and in cell lines derived from cervical cancer. , 1984, The EMBO journal.

[11]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[12]  E. Cesarman,et al.  Identification of herpesvirus-like DNA sequences in AIDS-associated Kaposi's sarcoma. , 1994, Science.

[13]  Timothy B. Stockwell,et al.  The Sequence of the Human Genome , 2001, Science.