Parallel construction of orthologous sequence-ready clone contig maps in multiple species.

@article{thomas02, abstract = {Comparison is a fundamental tool for analyzing DNA sequence. Interspecies sequence comparison is particularly powerful for inferring genome function and is based on the simple premise that conserved sequences are likely to be important. Thus, the comparison of a genomic sequence with its orthologous counterpart from another species is increasingly becoming an integral component of genome analysis. In ideal situations, such comparisons are performed with orthologous sequences from multiple species. To facilitate multispecies comparative sequence analysis, a robust and scalable strategy for simultaneously constructing sequence-ready bacterial artificial chromosome (BAC) contig maps from targeted genomic regions has been developed. Central to this approach is the generation and utilization of "universal" oligonucleotide-based hybridization probes ("overgo" probes), which are designed from sequences that are highly conserved between distantly related species. Large collections of these probes are used en masse to screen BAC libraries from multiple species in parallel, with the isolated clones assembled into physical contig maps. To validate the effectiveness of this strategy, efforts were focused on the construction of BAC-based physical maps from multiple mammalian species (chimpanzee, baboon, cat, dog, cow, and pig). Using available human and mouse genomic sequence and a newly developed computer program to design the requisite probes, sequence-ready maps were constructed in all species for a series of targeted regions totaling approximately 16 Mb in the human genome. The described approach can be used to facilitate the multispecies comparative sequencing of targeted genomic regions and can be adapted for constructing BAC contig maps in other vertebrates.}, address = {Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.}, author = {Thomas, J. W. and Prasad, A. B. and Summers, T. J. and Lin, Lee S. Q. and Maduro, V. V. and Idol, J. R. and Ryan, J. F. and Thomas, P. J. and Mcdowell, J. C. and Green, E. D. }, citeulike-article-id = {276974}, doi = {http://dx.doi.org/10.1101/gr.283202}, issn = {1088-9051}, journal = {Genome Res}, keywords = {bac, bac\_mapping, comparative\_genomics, map, overgo, physical, soop, zooseq}, month = {August}, number = {8}, pages = {1277--1285}, posted-at = {2005-08-08 22:09:03}, priority = {0}, title = {Parallel construction of orthologous sequence-ready clone contig maps in multiple species.}, url = {http://dx.doi.org/10.1101/gr.283202}, volume = {12}, year = {2002} }

TY - JOUR ID - thomas02 L3 - citeulike-article-id:276974 N2 - Comparison is a fundamental tool for analyzing DNA sequence. Interspecies sequence comparison is particularly powerful for inferring genome function and is based on the simple premise that conserved sequences are likely to be important. Thus, the comparison of a genomic sequence with its orthologous counterpart from another species is increasingly becoming an integral component of genome analysis. In ideal situations, such comparisons are performed with orthologous sequences from multiple species. To facilitate multispecies comparative sequence analysis, a robust and scalable strategy for simultaneously constructing sequence-ready bacterial artificial chromosome (BAC) contig maps from targeted genomic regions has been developed. Central to this approach is the generation and utilization of "universal" oligonucleotide-based hybridization probes ("overgo" probes), which are designed from sequences that are highly conserved between distantly related species. Large collections of these probes are used en masse to screen BAC libraries from multiple species in parallel, with the isolated clones assembled into physical contig maps. To validate the effectiveness of this strategy, efforts were focused on the construction of BAC-based physical maps from multiple mammalian species (chimpanzee, baboon, cat, dog, cow, and pig). Using available human and mouse genomic sequence and a newly developed computer program to design the requisite probes, sequence-ready maps were constructed in all species for a series of targeted regions totaling approximately 16 Mb in the human genome. The described approach can be used to facilitate the multispecies comparative sequencing of targeted genomic regions and can be adapted for constructing BAC contig maps in other vertebrates. IS - 8 JF - Genome Res SN - 1088-9051 AD - Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA. EP - 1285 TI - Parallel construction of orthologous sequence-ready clone contig maps in multiple species. VL - 12 SP - 1277 KW - bac KW - bac_mapping KW - comparative_genomics KW - map KW - overgo KW - physical KW - soop KW - zooseq AU - Thomas, JW AU - Prasad, AB AU - Summers, TJ AU - Lin, Lee AU - Maduro, VV AU - Idol, JR AU - Ryan, JF AU - Thomas, PJ AU - Mcdowell, JC AU - Green, ED PY - 2002/August// UR - http://dx.doi.org/10.1101/gr.283202 ER -