dna sequence analysis

Summary

Summary: A multistage process that includes DNA cloning, physical mapping, subcloning, sequencing, and information analysis.

Top Publications

  1. ncbi Initial sequencing and analysis of the human genome
    E S Lander
    Whitehead Institute for Biomedical Research, Center for Genome Research, Cambridge, Massachusetts 02142, USA
    Nature 409:860-921. 2001
  2. ncbi MatInspector and beyond: promoter analysis based on transcription factor binding sites
    K Cartharius
    Genomatix Software GmbH Landsberger Strasse 6, 80339 München, Germany
    Bioinformatics 21:2933-42. 2005
  3. ncbi TM4: a free, open-source system for microarray data management and analysis
    A I Saeed
    Institute for Genomic Research, Rockville, MD, USA
    Biotechniques 34:374-8. 2003
  4. ncbi A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    B M Bolstad
    Group in Biostatistics, University of California, Berkeley, CA 94720, USA
    Bioinformatics 19:185-93. 2003
  5. ncbi RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    Alexandros Stamatakis
    Swiss Federal Institute of Technology Lausanne, School of Computer and Communication Sciences Lab Prof Moret, Station 14, CH 1015 Lausanne, Switzerland
    Bioinformatics 22:2688-90. 2006
  6. pmc BEAST: Bayesian evolutionary analysis by sampling trees
    Alexei J Drummond
    Bioinformatics Institute, University of Auckland, Auckland, New Zealand
    BMC Evol Biol 7:214. 2007
  7. ncbi MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0
    Koichiro Tamura
    Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, AZ, USA
    Mol Biol Evol 24:1596-9. 2007
  8. pmc Velvet: algorithms for de novo short read assembly using de Bruijn graphs
    Daniel R Zerbino
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    Genome Res 18:821-9. 2008
  9. ncbi Haploview: analysis and visualization of LD and haplotype maps
    J C Barrett
    Whitehead Institute for Biomedical Research Cambridge, MA 02142, USA
    Bioinformatics 21:263-5. 2005
  10. pmc CAP3: A DNA sequence assembly program
    X Huang
    Department of Computer Science, Michigan Technological University, Houghton, Michigan 49931 USA
    Genome Res 9:868-77. 1999

Detail Information

Publications307 found, 100 shown here

  1. ncbi Initial sequencing and analysis of the human genome
    E S Lander
    Whitehead Institute for Biomedical Research, Center for Genome Research, Cambridge, Massachusetts 02142, USA
    Nature 409:860-921. 2001
    ..We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence...
  2. ncbi MatInspector and beyond: promoter analysis based on transcription factor binding sites
    K Cartharius
    Genomatix Software GmbH Landsberger Strasse 6, 80339 München, Germany
    Bioinformatics 21:2933-42. 2005
    ..The next steps in promoter analysis can be tackled only with reliable predictions, e.g. finding phylogenetically conserved patterns or identifying higher order combinations of sites in promoters of co-regulated genes...
  3. ncbi TM4: a free, open-source system for microarray data management and analysis
    A I Saeed
    Institute for Genomic Research, Rockville, MD, USA
    Biotechniques 34:374-8. 2003
  4. ncbi A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    B M Bolstad
    Group in Biostatistics, University of California, Berkeley, CA 94720, USA
    Bioinformatics 19:185-93. 2003
    ..Normalization is a process for reducing this variation. It is common to see non-linear relations between arrays and the standard normalization provided by Affymetrix does not perform well in these situations...
  5. ncbi RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    Alexandros Stamatakis
    Swiss Federal Institute of Technology Lausanne, School of Computer and Communication Sciences Lab Prof Moret, Station 14, CH 1015 Lausanne, Switzerland
    Bioinformatics 22:2688-90. 2006
    ..The program has been used to compute ML trees on two of the largest alignments to date containing 25,057 (1463 bp) and 2182 (51,089 bp) taxa, respectively...
  6. pmc BEAST: Bayesian evolutionary analysis by sampling trees
    Alexei J Drummond
    Bioinformatics Institute, University of Auckland, Auckland, New Zealand
    BMC Evol Biol 7:214. 2007
    ..A large number of popular stochastic models of sequence evolution are provided and tree-based models suitable for both within- and between-species sequence data are implemented...
  7. ncbi MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0
    Koichiro Tamura
    Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, AZ, USA
    Mol Biol Evol 24:1596-9. 2007
    ..The current version of MEGA is available free of charge at (http://www.megasoftware.net)...
  8. pmc Velvet: algorithms for de novo short read assembly using de Bruijn graphs
    Daniel R Zerbino
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    Genome Res 18:821-9. 2008
    ..Velvet represents a new approach to assembly that can leverage very short reads in combination with read pairs to produce useful assemblies...
  9. ncbi Haploview: analysis and visualization of LD and haplotype maps
    J C Barrett
    Whitehead Institute for Biomedical Research Cambridge, MA 02142, USA
    Bioinformatics 21:263-5. 2005
    ..Haploview is a software package that provides computation of linkage disequilibrium statistics and population haplotype patterns from primary genotype data in a visually appealing and interactive interface...
  10. pmc CAP3: A DNA sequence assembly program
    X Huang
    Department of Computer Science, Michigan Technological University, Houghton, Michigan 49931 USA
    Genome Res 9:868-77. 1999
    ..PHRAP often produces longer contigs than CAP3 whereas CAP3 often produces fewer errors in consensus sequences than PHRAP. It is easier to construct scaffolds with CAP3 than with PHRAP on low-pass data with forward-reverse constraints...
  11. pmc Tandem repeats finder: a program to analyze DNA sequences
    G Benson
    Department of Biomathematical Sciences, Mount Sinai School of Medicine, New York, NY 10029 6574, USA
    Nucleic Acids Res 27:573-80. 1999
    ..These sequences range in size from 3 kb up to 700 kb. A World Wide Web server interface atc3.biomath.mssm.edu/trf.html has been established for automated use of the program...
  12. pmc Fast and accurate short read alignment with Burrows-Wheeler transform
    Heng Li
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
    Bioinformatics 25:1754-60. 2009
    ..The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals...
  13. pmc Genome sequencing in microfabricated high-density picolitre reactors
    Marcel Margulies
    454 Life Sciences Corp, 20 Commercial Street, Branford, Connecticut 06405, USA
    Nature 437:376-80. 2005
    ..Here we show the utility, throughput, accuracy and robustness of this system by shotgun sequencing and de novo assembly of the Mycoplasma genitalium genome with 96% coverage at 99.96% accuracy in one run of the machine...
  14. ncbi Artemis: sequence visualization and annotation
    K Rutherford
    The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Bioinformatics 16:944-5. 2000
    ..Sequences and annotation can be read and written directly in EMBL, GenBank and GFF format. AVAILABITLTY: Artemis is available under the GNU General Public License from http://www.sanger.ac.uk/Software/Artemis..
  15. pmc MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences
    Sudhir Kumar
    Biodesign Institute, A240, Arizona State University, Tempe, AZ 85287 5301, USA
    Brief Bioinform 9:299-306. 2008
    ..We also discuss how MEGA might evolve in the future to assist researchers in their growing need to analyze large data set using new computational methods...
  16. pmc InterProScan: protein domains identifier
    E Quevillon
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 33:W116-20. 2005
    ..O'Reilly Publishers, Sebastopol, CA, http://www.w3.org/TR/soap/] are also available to the users. Various output formats are supported and include text tables, XML documents, as well as various graphs to help interpret the results...
  17. pmc ARB: a software environment for sequence data
    Wolfgang Ludwig
    Lehrstuhl fur Mikrobiologie, Technische Universitat Munchen, D 853530 Freising, Germany
    Nucleic Acids Res 32:1363-71. 2004
    ..Currently, the package is used by numerous working groups worldwide...
  18. ncbi SOAP: short oligonucleotide alignment program
    Ruiqiang Li
    Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China
    Bioinformatics 24:713-4. 2008
    ..SOAP is a command-driven program, which supports multi-threaded parallel computing, and has a batch module for multiple query sets...
  19. ncbi ACT: the Artemis Comparison Tool
    Tim J Carver
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Bioinformatics 21:3422-3. 2005
    ..ACT is part of the Artemis distribution and is similarly open source, written in Java and can run on any Java enabled platform, including UNIX, Macintosh and Windows...
  20. pmc Microbial diversity in the deep sea and the underexplored "rare biosphere"
    Mitchell L Sogin
    Josephine Bay Paul Center, Marine Biological Laboratory at Woods Hole, 7 MBL Street, Woods Hole, MA 02543, USA
    Proc Natl Acad Sci U S A 103:12115-20. 2006
    ..Members of the rare biosphere are highly divergent from each other and, at different times in earth's history, may have had a profound impact on shaping planetary processes...
  21. ncbi The consensus coding sequences of human breast and colorectal cancers
    Tobias Sjoblom
    Ludwig Center and Howard Hughes Medical Institute, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA
    Science 314:268-74. 2006
    ..These data define the genetic landscape of two human cancer types, provide new targets for diagnostic and therapeutic intervention, and open fertile avenues for basic research in tumor biology...
  22. ncbi An obesity-associated gut microbiome with increased capacity for energy harvest
    Peter J Turnbaugh
    Center for Genome Sciences, Washington University, St Louis, Missouri 63108, USA
    Nature 444:1027-31. 2006
    ..These results identify the gut microbiota as an additional contributing factor to the pathophysiology of obesity...
  23. ncbi The complete genome sequence of Escherichia coli K-12
    F R Blattner
    Laboratory of Genetics, University of Wisconsin Madison, 445 Henry Mall, Madison, WI 53706, USA
    Science 277:1453-62. 1997
    ..The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer...
  24. pmc Identifying bacterial genes and endosymbiont DNA with Glimmer
    Arthur L Delcher
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Bioinformatics 23:673-9. 2007
    ..This module was developed in response to the discovery that eukaryotic genome sequencing projects sometimes inadvertently capture the DNA of intracellular bacteria living in the host...
  25. ncbi Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
    S T Cole
    Sanger Centre, Wellcome Trust Genome Campus, Hinxton, UK
    Nature 393:537-44. 1998
    ....
  26. pmc PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
    Mikita Suyama
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Nucleic Acids Res 34:W609-12. 2006
    ..Another distinct feature is that the user can specify a subregion of the input alignment in order to specifically analyze functional domains or exons of interest. The PAL2NAL server is available at http://www.bork.embl.de/pal2nal...
  27. ncbi Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing
    J Cristobal Vera
    Department of Biology, 208 Mueller Laboratory, Pennsylvania State University, University Park, PA 16802, USA
    Mol Ecol 17:1636-47. 2008
    ..This development narrows the gap between approaches based on model organisms with rich genetic resources vs. species that are most tractable for ecological and evolutionary studies...
  28. pmc Accuracy and quality of massively parallel DNA pyrosequencing
    Susan M Huse
    Josephine Bay Paul Center, Marine Biological Laboratory at Woods Hole, MBL Street, Woods Hole, MA 02543, USA
    Genome Biol 8:R143. 2007
    ....
  29. pmc Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms
    Peter A C 't Hoen
    The Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
    Nucleic Acids Res 36:e141. 2008
    ..We conclude that deep sequencing provides a major advance in robustness, comparability and richness of expression profiling data and is expected to boost collaborative, comparative and integrative genomics studies...
  30. ncbi TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets
    Geo Pertea
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Bioinformatics 19:651-2. 2003
    ..The system can run on multi-CPU architectures including SMP and PVM...
  31. pmc The human microbiome project
    Peter J Turnbaugh
    Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri 63108, USA
    Nature 449:804-10. 2007
    ..A strategy to understand the microbial components of the human genetic and metabolic landscape and how they contribute to normal physiology and predisposition to disease...
  32. pmc Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
    Juliane C Dohm
    Max Planck Institute for Molecular Genetics, Ihnestr 63 73, 14195 Berlin, Germany
    Nucleic Acids Res 36:e105. 2008
    ..Such biases have implications on the use and interpretation of Solexa data, for de novo sequencing, re-sequencing, the identification of single nucleotide polymorphisms and DNA methylation sites, as well as for transcriptome analysis...
  33. pmc Phylogeny.fr: robust phylogenetic analysis for the non-specialist
    A Dereeper
    Information Génomique et Structurale IGS, CNRS UPR2589, IFR 88, Marseille, France
    Nucleic Acids Res 36:W465-9. 2008
    ..A guide tree then helps to select neighbor sequences to be used as input for the phylogeny pipeline. Phylogeny.fr is available at: http://www.phylogeny.fr/..
  34. pmc High-throughput functional annotation and data mining with the Blast2GO suite
    Stefan Götz
    Bioinformatics Department, Centro de Investigacion Principe Felipe, Valencia, Spain
    Nucleic Acids Res 36:3420-35. 2008
    ..Our aim is to offer biologists useful information to take into account when addressing the task of functionally characterizing their sequence data...
  35. pmc Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
    Shawn J Cokus
    Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA
    Nature 452:215-9. 2008
    ....
  36. pmc Genome sequence of Aedes aegypti, a major arbovirus vector
    Vishvanath Nene
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 316:1718-23. 2007
    ..An increase in genes encoding odorant binding, cytochrome P450, and cuticle domains relative to An. gambiae suggests that members of these protein families underpin some of the biological differences between the two mosquito species...
  37. ncbi The genome of the African trypanosome Trypanosoma brucei
    Matthew Berriman
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
    Science 309:416-22. 2005
    ..brucei and the greatest in L. major. Horizontal transfer of genes of bacterial origin has contributed to some of the metabolic differences in these parasites, and a number of novel potential drug targets have been identified...
  38. ncbi The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
    Olivier Jaillon
    Genoscope CEA and UMR 8030 CNRS Genoscope Université d Evry, 2 rue Gaston Cremieux, BP5706, 91057 Evry, France
    Nature 449:463-7. 2007
    ..Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants...
  39. pmc Accurate whole human genome sequencing using reversible terminator chemistry
    David R Bentley
    Illumina Cambridge Ltd Formerly Solexa Ltd, Chesterford Research Park, Little Chesterford, Nr Saffron Walden, Essex CB10 1XL, UK
    Nature 456:53-9. 2008
    ..Our approach is effective for accurate, rapid and economical whole-genome re-sequencing and many other biomedical applications...
  40. ncbi GMAP: a genomic mapping and alignment program for mRNA and EST sequences
    Thomas D Wu
    Department of Bioinformatics Genentech, Inc, South San Francisco, CA 94080, USA
    Bioinformatics 21:1859-75. 2005
    ....
  41. pmc Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx
    Eli Meyer
    University of Texas at Austin, 1 University Station C0930, Austin, TX 78712, USA
    BMC Genomics 10:219. 2009
    ..We have applied these methods to sequence the transcriptome of planulae larvae from the coral Acropora millepora...
  42. ncbi The genomic landscapes of human breast and colorectal cancers
    Laura D Wood
    Ludwig Center for Cancer Genetics and Therapeutics and Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA
    Science 318:1108-13. 2007
    ..These results have implications for understanding the nature and heterogeneity of human cancers and for using personal genomics for tumor diagnosis and therapy...
  43. ncbi Initial sequencing and comparative analysis of the mouse genome
    Robert H Waterston
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 420:520-62. 2002
    ....
  44. pmc An integrated software system for analyzing ChIP-chip and ChIP-seq data
    Hongkai Ji
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland 21205, USA
    Nat Biotechnol 26:1293-300. 2008
    ....
  45. pmc PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
    Joel Rozowsky
    Molecular Biophysics and Biochemistry Dept, Yale University, PO Box 208114, New Haven, Connecticut 06520 8114, USA
    Nat Biotechnol 27:66-75. 2009
    ..Our scoring procedure enables us to optimize experimental design by estimating the depth of sequencing required for a desired level of coverage and demonstrating that more than two replicates provides only a marginal gain in information...
  46. ncbi Datamonkey: rapid detection of selective pressure on individual sites of codon alignments
    Sergei L Kosakovsky Pond
    Antiviral Research Center, University of California, San Diego, CA 92103, USA
    Bioinformatics 21:2531-3. 2005
    ..The methods range from very fast data exploration to the some of the most complex models available in public domain software, and are implemented to run in parallel on a cluster of computers...
  47. pmc High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome
    Evandro Novaes
    School of Forest Resources and Conservation, University of Florida, PO Box 110410, Gainesville, USA
    BMC Genomics 9:312. 2008
    ..However, it is questionable how effective the sequencing of large numbers of short reads for species with essentially no prior gene sequence information will support contig assemblies and sequence annotation...
  48. pmc MEME SUITE: tools for motif discovery and searching
    Timothy L Bailey
    Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
    Nucleic Acids Res 37:W202-8. 2009
    ..All of the motif-based tools are now implemented as web services via Opal. Source code, binaries and a web server are freely available for noncommercial use at http://meme.nbcr.net...
  49. pmc Personalized copy number and segmental duplication maps using next-generation sequencing
    Can Alkan
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
    Nat Genet 41:1061-7. 2009
    ..2 x 10(-16)). Our method can distinguish between different copies of highly identical genes, providing a more accurate assessment of gene content and insight into functional constraint without the limitations of array-based technology...
  50. ncbi Genome-wide mapping of in vivo protein-DNA interactions
    David S Johnson
    Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305 5120, USA
    Science 316:1497-502. 2007
    ..96] and statistical confidence (P <10(-4)), properties that were important for inferring new candidate interactions. These include key transcription factors in the gene network that regulates pancreatic islet cell development...
  51. pmc Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex
    Micah Hamady
    Department of Computer Science, UCB 430, University of Colorado, Boulder, Colorado 80309, USA
    Nat Methods 5:235-7. 2008
    ....
  52. pmc Automated generation of heuristics for biological sequence comparison
    Guy St C Slater
    The Ensembl Group, EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    BMC Bioinformatics 6:31. 2005
    ....
  53. ncbi SOAP2: an improved ultrafast tool for short read alignment
    Ruiqiang Li
    Beijing Genomics Institute at Shenzhen, Shenzhen, 518083, China
    Bioinformatics 25:1966-7. 2009
    ..Additionally, this tool now supports multiple text and compressed file formats. A consensus builder has also been developed for consensus assembly and SNP detection from alignment of short reads on a reference genome...
  54. ncbi Real-time DNA sequencing from single polymerase molecules
    JOHN EID
    Pacific Biosciences, 1505 Adams Drive, Menlo Park, CA 94025, USA
    Science 323:133-8. 2009
    ..Consensus sequences were generated from the single-molecule reads at 15-fold coverage, showing a median accuracy of 99.3%, with no systematic error beyond fluorophore-dependent error rates...
  55. pmc NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
    Kim D Pruitt
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Rm 6An 12J, 45 Center Drive, Bethesda, MD 20892 6510, USA
    Nucleic Acids Res 35:D61-5. 2007
    ..The format of all RefSeq records is validated, and an increasing number of tests are being applied to evaluate the quality of sequence and annotation, especially in the context of complete genomic sequence...
  56. pmc Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing
    Andreas Gnirke
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Biotechnol 27:182-9. 2009
    ..One lane of Illumina sequence was sufficient to call high-confidence genotypes for 89% of the targeted exon space...
  57. ncbi Applications of next-generation sequencing technologies in functional genomics
    Olena Morozova
    BC Cancer Agency Genome Sciences Centre, Vancouver, BC, Canada
    Genomics 92:255-64. 2008
    ..This review discusses applications of next-generation sequencing technologies in functional genomics research and highlights the transforming potential these technologies offer...
  58. ncbi Next-generation sequencing transforms today's biology
    Stephan C Schuster
    Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, 310 Wartik Building, University Park, Pennsylvania 16802, USA
    Nat Methods 5:16-8. 2008
    ..However, before stepping into the limelight, next-generation sequencing had to overcome the inertia of a field that relied on Sanger-sequencing for 30 years...
  59. pmc Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor
    Oleksiy Kohany
    Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA 94043, USA
    BMC Bioinformatics 7:474. 2006
    ..Updating and maintenance of the database requires specialized tools, which we have created and made available for use with Repbase, and which may be useful as a template for other curated databases...
  60. ncbi A metagenomic survey of microbes in honey bee colony collapse disorder
    Diana L Cox-Foster
    Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA
    Science 318:283-7. 2007
    ..One organism, Israeli acute paralysis virus of bees, was strongly correlated with CCD...
  61. ncbi The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)
    G A Tuskan
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Science 313:1596-604. 2006
    ..Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport...
  62. pmc A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters
    Serge Saxonov
    Biomedical Informatics Program, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 103:1412-7. 2006
    ....
  63. ncbi A phylogenomic study of birds reveals their evolutionary history
    Shannon J Hackett
    Zoology Department, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA
    Science 320:1763-8. 2008
    ..Our results provide a valuable resource for phylogenetic and comparative studies in birds...
  64. pmc VISTA: computational tools for comparative genomics
    Kelly A Frazer
    Perlegen Sciences, Inc, 2021 Stierlin Court, Mountain View, CA 94043, USA
    Nucleic Acids Res 32:W273-9. 2004
    ..We illustrate capabilities of the VISTA site by the analysis of a 180 kb interval on human chromosome 5 that encodes for the kinesin family member 3A (KIF3A) protein...
  65. pmc Mapping short DNA sequencing reads and calling variants using mapping quality scores
    Heng Li
    The Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
    Genome Res 18:1851-8. 2008
    ..Both read mapping and genotype calling are evaluated on simulated data and real data. MAQ is accurate, efficient, versatile, and user-friendly. It is freely available at http://maq.sourceforge.net...
  66. pmc Evaluation of methods for detecting recombination from DNA sequences: computer simulations
    D Posada
    Department of Zoology, Brigham Young University, Provo, UT 84602, USA
    Proc Natl Acad Sci U S A 98:13757-62. 2001
    ..Results shown here will provide some guidance in the selection of the most appropriate method/s for the analysis of the particular data at hand...
  67. ncbi Next-generation DNA sequencing
    Jay Shendure
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195 5065, USA
    Nat Biotechnol 26:1135-45. 2008
    ....
  68. pmc Exome sequencing identifies the cause of a mendelian disorder
    Sarah B Ng
    Department of Genome Sciences, University of Washington, Seattle, Washington, USA
    Nat Genet 42:30-5. 2010
    ..Exome sequencing of a small number of unrelated affected individuals is a powerful, efficient strategy for identifying the genes underlying rare mendelian disorders and will likely transform the genetic analysis of monogenic traits...
  69. ncbi The genome sequence of the filamentous fungus Neurospora crassa
    James E Galagan
    Whitehead Institute Center for Genome Research, 320 Charles Street, Cambridge, Massachusetts 02141, USA
    Nature 422:859-68. 2003
    ..Genome analysis suggests that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes...
  70. pmc Distribution and intensity of constraint in mammalian genomic sequence
    Gregory M Cooper
    Department of Genetics, Stanford University, Stanford, California 94305, USA
    Genome Res 15:901-13. 2005
    ..We anticipate that GERP and the types of analyses it facilitates will provide further insights and improved annotation for the human genome as mammalian genome sequence data become richer...
  71. pmc Comparative analysis of human gut microbiota by barcoded pyrosequencing
    Anders F Andersson
    Swedish Institute for Infectious Disease Control, Solna, Sweden
    PLoS ONE 3:e2836. 2008
    ..Here we applied the technique to analyze microbial communities in throat, stomach and fecal samples. Our results demonstrate the applicability of barcoded pyrosequencing as a high-throughput method for comparative microbial ecology...
  72. ncbi Complete genome sequence of Salmonella enterica serovar Typhimurium LT2
    M McClelland
    Sidney Kimmel Cancer Center, 10835 Altman Row, San Diego, California 92121, USA
    Nature 413:852-6. 2001
    ..Most of these homologues were previously unknown, and 50 may be exported to the periplasm or outer membrane, rendering them accessible as therapeutic or vaccine targets...
  73. ncbi Sequence-based species delimitation for the DNA taxonomy of undescribed insects
    Joan Pons
    Department of Entomology, The Natural History Museum, London SW7 5BD, United Kingdom
    Syst Biol 55:595-609. 2006
    ....
  74. pmc A large genome center's improvements to the Illumina sequencing system
    Michael A Quail
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
    Nat Methods 5:1005-10. 2008
    ....
  75. ncbi Gene prediction with a hidden Markov model and a new intron submodel
    Mario Stanke
    Institut fur Mikrobiologie und Genetik, Abteilung Bioinformatik, Universitat Gottingen, Gottingen, Germany
    Bioinformatics 19:ii215-25. 2003
    ..Gene finding programs have achieved relatively high accuracy on short genomic sequences but do not perform well on longer sequences with an unknown number of genes in them. Here existing programs tend to predict many false exons...
  76. pmc Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing
    Susan M Huse
    Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
    PLoS Genet 4:e1000255. 2008
    ..This technique allows the cost-effective exploration of changes in microbial community structure, including the rare biosphere, over space and time and can be applied immediately to initiatives, such as the Human Microbiome Project...
  77. ncbi Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA
    R M Andrews
    Nat Genet 23:147. 1999
  78. ncbi Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome
    Michael Weber
    Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH 4058 Basel, Switzerland
    Nat Genet 39:457-66. 2007
    ..Moreover, we observe that inactive unmethylated CpG island promoters show elevated levels of dimethylation of Lys4 of histone H3, suggesting that this chromatin mark may protect DNA from methylation...
  79. ncbi Community genomics among stratified microbial assemblages in the ocean's interior
    Edward F DeLong
    Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Science 311:496-503. 2006
    ..Comparative genomic analyses of stratified microbial communities have the potential to provide significant insight into higher-order community organization and dynamics...
  80. pmc ABySS: a parallel assembler for short read sequence data
    Jared T Simpson
    Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada
    Genome Res 19:1117-23. 2009
    ..Analysis of these contigs identified polymorphic and novel sequences not present in the human reference assembly, which were validated by alignment to alternate human assemblies and to other primate genomes...
  81. ncbi Consed: a graphical tool for sequence finishing
    D Gordon
    Department of Molecular Biotechnology, University of Washington, Seattle, Washington 98195 7730, USA
    Genome Res 8:195-202. 1998
    ..More information is available at http:// www.genome.washington.edu/consed/consed. html...
  82. pmc Design and analysis of ChIP-seq experiments for DNA-binding proteins
    Peter V Kharchenko
    Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck St, Boston, Massachusetts 02115, USA
    Nat Biotechnol 26:1351-9. 2008
    ..We also analyze the relationship between the depth of sequencing and characteristics of the detected binding positions, and provide a method for estimating the sequencing depth necessary for a desired coverage of protein binding sites...
  83. ncbi Complete genome sequence of a virulent isolate of Streptococcus pneumoniae
    H Tettelin
    The Institute for Genomic Research (TIGR, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 293:498-506. 2001
    ..Comparative genome hybridization with DNA arrays revealed strain differences in S. pneumoniae that could contribute to differences in virulence and antigenicity...
  84. pmc High-resolution mapping and characterization of open chromatin across the genome
    Alan P Boyle
    Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
    Cell 132:311-22. 2008
    ..In addition, and unexpectedly, our analyses have uncovered detailed features of nucleosome structure...
  85. ncbi TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders
    W H Majoros
    Bioinformatics Department, The Institute for Genomic Research, Rockville, MD 20850, USA
    Bioinformatics 20:2878-9. 2004
    ..Both programs have been used at TIGR for the annotation of the Aspergillus fumigatus and Toxoplasma gondii genomes...
  86. pmc Biological identifications through DNA barcodes
    Paul D N Hebert
    Department of Zoology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
    Proc Biol Sci 270:313-21. 2003
    ..Its assembly will also generate important new insights into the diversification of life and the rules of molecular evolution...
  87. pmc Evaluation of next generation sequencing platforms for population targeted sequencing studies
    Olivier Harismendy
    Scripps Genomic Medicine, Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, USA
    Genome Biol 10:R32. 2009
    ..To evaluate these platforms for this application, we analyzed human sequence generated by the Roche 454, Illumina GA, and the ABI SOLiD technologies for the same 260 kb in four individuals...
  88. pmc Targeted capture and massively parallel sequencing of 12 human exomes
    Sarah B Ng
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Nature 461:272-6. 2009
    ..This strategy may be extendable to diseases with more complex genetics through larger sample sizes and appropriate weighting of non-synonymous variants by predicted functional impact...
  89. pmc Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification by single-genome amplification and sequencing
    Jesus F Salazar-Gonzalez
    Department of Medicine, University of Alabama at Birmingham, 720 20th Street South, Kaul 816, Birmingham, AL 35294, USA
    J Virol 82:3952-70. 2008
    ....
  90. pmc Tablet--next generation sequence assembly visualization
    Iain Milne
    Genetics Programme, Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UK
    Bioinformatics 26:401-2. 2010
    ..Tablet is both multi-core aware and memory efficient, allowing it to handle assemblies containing millions of reads, even on a 32-bit desktop machine...
  91. pmc Comparative genomics of the neglected human malaria parasite Plasmodium vivax
    Jane M Carlton
    The Institute for Genomic Research J Craig Venter Institute, 9704 Medical Research Drive, Rockville, Maryland 20850, USA
    Nature 455:757-63. 2008
    ..Completion of the P. vivax genome provides the scientific community with a valuable resource that can be used to advance investigation into this neglected species...
  92. pmc The Ensembl genome database project
    T Hubbard
    The Wellcome Trust Sanger Institute and European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Nucleic Acids Res 30:38-41. 2002
    ..The Ensembl system is being installed around the world in both companies and academic sites on machines ranging from supercomputers to laptops...
  93. ncbi The impact of next-generation sequencing technology on genetics
    Elaine R Mardis
    Genome Sequencing Center, Washington University School of Medicine, St Louis, MO 63108, USA
    Trends Genet 24:133-41. 2008
    ..Here I survey next-generation sequencing technologies and consider how they can provide a more complete picture of how the genome shapes the organism...
  94. ncbi SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries
    Curtis P van Tassell
    Bovine Functional Genomics Laboratory, United States Department of Agriculture, Agricultural Research Service, 10300 Baltimore Avenue, Beltsville, Maryland 20705, USA
    Nat Methods 5:247-52. 2008
    ..67. This approach for simultaneous de novo discovery of high-quality SNPs and population characterization of allele frequencies may be applied to any species with at least a partially sequenced genome...
  95. ncbi Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
    Weizhong Li
    Burnham Institute for Medical Research La Jolla, CA 92037, USA
    Bioinformatics 22:1658-9. 2006
    ..All these programs can handle huge datasets with millions of sequences and can be hundreds of times faster than methods based on the popular sequence comparison and database search tools, such as BLAST...
  96. pmc Short pyrosequencing reads suffice for accurate microbial community analysis
    Zongzhi Liu
    Department of Chemistry and Biochemistry, UCB 215, University of Colorado at Boulder, Boulder, CO 80309 0215, USA
    Nucleic Acids Res 35:e120. 2007
    ....
  97. pmc MEME: discovering and analyzing DNA and protein sequence motifs
    Timothy L Bailey
    Institute of Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
    Nucleic Acids Res 34:W369-73. 2006
    ..This article describes the freely accessible web server and its architecture, and discusses ways to use MEME effectively to find new sequence patterns in biological sequences and analyze their significance...
  98. ncbi The uncultured microbial majority
    Michael S Rappé
    Department of Microbiology, Oregon State University, Corvallis, Oregon 97331, USA
    Annu Rev Microbiol 57:369-94. 2003
    ..Genome sequence information that would allow ribosomal RNA gene trees to be related to broader patterns in microbial genome evolution is scant, and therefore microbial diversity remains largely unexplored territory...
  99. pmc Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential
    S Temnykh
    Department of Plant Breeding, USDA-ARS Center for Agricultural Bioinformatics, Cornell University, Ithaca, New York 14853-1901, USA
    Genome Res 11:1441-52. 2001
    ..This contribution brings the number of microsatellite markers that have been rigorously evaluated for amplification, map position, and allelic diversity in Oryza spp. to a total of 500...
  100. ncbi Java Treeview--extensible visualization of microarray data
    Alok J Saldanha
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Bioinformatics 20:3246-8. 2004
    ..An applet version is also available that can be used on any website with no special server-side setup...
  101. pmc An Eulerian path approach to DNA fragment assembly
    P A Pevzner
    Department of Computer Science and Engineering, University of California, San Diego, La Jolla, USA
    Proc Natl Acad Sci U S A 98:9748-53. 2001
    ..euler, in contrast to the celera assembler, does not mask such repeats but uses them instead as a powerful fragment assembly tool...

Research Grants63

  1. Forward Genetics to Identify Complex Gene Interactions Involved in Glaucoma
    Elena V Semina; Fiscal Year: 2010
    ..Using forward genetics in zebrafish and pedigree/patient DNA sequence analysis in humans, we will identify complex genetic interactions that contribute to phenotypes associated with ..
  2. Cloning &Functional Studies of Deafness Mutations
    Kenneth R Johnson; Fiscal Year: 2013
    ..mutations or hearing-related genes will be tested for potential allelism by functional complementation and DNA sequence analysis, and those that map to new locations will become subjects for future positional cloning efforts to ..
  3. Oxidant Stress Mechanisms in Preeclampsia
    Scott W Walsh; Fiscal Year: 2013
    ..will be evaluated in vessels from women with normal pregnancies and women with preeclampsia by bisulfite DNA sequence analysis and COBRA (Combined Bisulfite Restriction Analysis)...
  4. MOLECULAR &CELLULAR MECHANISMS IN TRANSFUSION MEDICINE
    Peter J Newman; Fiscal Year: 2013
    ..The Shared Instrumentation Core will continue to provide centralized instrumentation and expertise for DNA sequence analysis, peptide synthesis, image analysis, histology, flow cytometry, BIAcore analysis, and monoclonal antibody ..
  5. Aging and the unstable epigenome
    Gerd P Pfeifer; Fiscal Year: 2013
    ..Genome-wide analysis will be accomplished by microarray and high throughput DNA sequence analysis. This grant proposes an in-depth analysis of the epigenome, at the level of histone modifications, DNA ..
  6. Molecular basis of Pseudomonas aeruginosa persistence in chronic wound infections
    Soyeon Lippman; Fiscal Year: 2013
    ..Tn-seq utilizes massively parallel DNA sequence analysis to track millions of bacteria carrying unique transposon insertion mutations...
  7. High Performance Validation and Classification of Metagenomic Ribosomal-RNA Seque
    Daniel Frank; Fiscal Year: 2011
    ..In this project, we propose to build a software infrastructure based on a high-precision DNA sequence analysis tool (INFERNAL), that addresses many of the critical barriers to progress currently facing researchers in ..
  8. Mutational analysis of the vlp/vsp antigenic variation system of the relapsing fe
    TROY MICHAEL BANKHEAD; Fiscal Year: 2013
    ..Previous studies involving DNA sequence analysis of Borrelia hermsii serotypes, the species endemic to the western United States, have implicated the ..
  9. Molecular genetic analysis of tyrosine kinases in myeloproliferative disorders
    Ross L Levine; Fiscal Year: 2010
    ..The Specific Aims are: 1. To use DNA sequence analysis to identify mutations in conserved domains of tyrosine kinases. 2...
  10. Sequence Variations in Low Copy Repeats on 22q11.2
    Bernice E Morrow; Fiscal Year: 2010
    ..We propose to define unstable regions on 22q11.2 by DNA sequence analysis. This will enable us to understand why chromosomes can rearrange during meiosis resulting in loss or gains ..
  11. Therapeutic intervention for Brucella
    AMY RAMBOW LARSEN; Fiscal Year: 2009
    ..b>DNA sequence analysis and direct peptide ? sequencing have shown that the sequence of the peptide prior to posttranslational ..
  12. Optimizing Genetic Testing for Deafness for Clinical Diagnostics
    Richard J H Smith; Fiscal Year: 2013
    ..generation and analysis for deafness genetic testing Goal 1: Comprehensive, high-throughput, low-cost DNA sequence analysis for genetic testing for deafness is possible at sensitivities and specificities comparable to Sanger ..
  13. Predicting Transcriptional and Epigenetic Networks in Cancer from Sequencing Data
    Jun S Song; Fiscal Year: 2013
    ..identify and experimentally validate cooperating factors of MITF by combining ChIP-seq data with DNA sequence analysis;(3) We will develop and apply statistical methods for inferring the epigenetic changes that are both ..
  14. Deep sequencing studies for cannabis and stimulant dependence
    Kirk C Wilhelmsen; Fiscal Year: 2013
    ..The technology and economics of DNA sequence analysis is rapidly evolving...
  15. Genotype Analysis for Diagnosis of Urea Cycle Disorders
    Steven Dobrowolski; Fiscal Year: 2007
    ..Melt profiling identifies regions containing sequence variants such that DNA sequence analysis is selectively targeted...
  16. Investigation of Cloud Computing to Support Data-Parallel Health Research
    Geoffrey C Fox; Fiscal Year: 2010
    ..biology, particularly widely encountered, "data parallel" problems including but not limited to DNA sequence analysis. GO funds will be used to establish the new field of Cloud-based computational life science...
  17. LIGNIN BIODEGRADATON--LIGNINASE & GLUCOSE OXIDASE GENES
    CA REDDY; Fiscal Year: 1992
    ..The data obtained will additionally be useful in producing genetically engineered strains of P. chrysosporium that give high yields of ligninase, an enzyme with many important practical applications...
  18. Novel Analytic Methods for Rare Variant Detection in Bipolar Disorder
    Mehdi Pirooznia; Fiscal Year: 2013
    ..by applicant): This proposal aims at training an MD/PhD bioinformatician in the statistical genetics of DNA sequence analysis, and in psychiatric genetics more generally, through a project that takes a novel approach to analyzing ..
  19. Ex Cyto DNA Sequencing from Single Bacterial Colonies
    DAVID ALAN MEAD; Fiscal Year: 2010
    ..Despite improvements in speed and reduction in costs of DNA sequence analysis, the process is still time, labor, and cost-intensive...
  20. E COLI PATHOGENICITY ISLANDS
    RODNEY WELCH; Fiscal Year: 1999
    ..b>DNA sequence analysis of the two PAIs provide significant matches to previously characterized virulence genes and mobile genetic ..
  21. FABRY DISEASE: MOLECULAR AND MODEL THERAPEUTIC STUDIES
    ROBERT DESNICK; Fiscal Year: 1991
    ..and cDNA clones are currently being screened and the segments hybridizing to the probes will be used for DNA sequence analysis. We anticipate that one or more of the clones already isolated will be shown to contain Alpha-Gal A ..
  22. PATHOGENESIS OF FELINE LEUKEMIA VIRUS INDUCED AIDS
    Edward Hoover; Fiscal Year: 1993
    ..By restriction site mapping molecular cloning, DNA sequence analysis, and in vitro and in vivo analysis of constructed viral chimeras, we have identified the immunodeficiency ..
  23. GENETIC AND BIOCHEMICAL ANALYSIS OF A MURINE RETROPOSON
    Sandra Martin; Fiscal Year: 1992
    ..Genetic considerations and DNA sequence analysis suggest that L1 is an active transposable element in mice and other mammals; its movement provides a major ..
  24. DNA SEQUENCE ANALYSIS OF EUCARYOTIC CYTOCHROME C GENES
    Ray Wu; Fiscal Year: 1990
    ..We plan to study more genes and pseudogenes by using a new approach for the identification of a functional gene from among many pseudogenes...
  25. KINASE FUNCTION DURING C ELEGANS MUSCLE DEVELOPMENT
    Benjamin Williams; Fiscal Year: 2004
    ..altered by the existing pat-4 mutations? All four existing pat-4 mutant alleles will be characterized by DNA sequence analysis. 3...
  26. TRANSFORMING GENES IN INHALATION CARCINOGENESIS
    Seymour Garte; Fiscal Year: 1991
    ..Once the novel nasal tumor oncogenes have been cloned, they will be characterized by DNA sequence analysis and their chromosomal location, levels of expression in various tissues and mechanism(s) of activation ..
  27. REGULATION & FUNCTION OF CALCIUM TRANSPORTING ATPASES
    GARY SHULL; Fiscal Year: 1993
    ..The genes will be characterized by restriction mapping, blot hybridization and DNA sequence analysis. Potential regulatory regions will be examined by DNase footprinting and band retardation assays to ..
  28. SEQUENCING HUMAN CHROMOSOME 22 CENTROMERE TO NF2
    Bruce Roe; Fiscal Year: 1999
    ..2. To continue to develop, improve and implement the automated procedures for DNA isolation, DNA sequence analysis, data acquisition, and data analysis, thereby increasing our DNA sequencing efficiency. 3...
  29. Variant detection and variant analysis process for diagnosis of CH and MODY
    David Margulies; Fiscal Year: 2006
    ..Such deletions are not detectable by direct Sanger DNA sequence analysis of genomic DNA if they span an entire PCR-amplification fragment (amplicon) since sequence is still ..
  30. AUTOMATED DNA ANALYSIS SYSTEM
    TERRI KINZY; Fiscal Year: 2001
    ..Trained personnel of the core facility will run and maintain all equipment to ensure optimal quality and speed. These personnel will also provide ongoing technical support to all users of this equipment. ..
  31. CHARACTERIZATION OF A PUTATIVE MOUSE EMBRYONIC GPDH GENE
    ROBERT IRELAND; Fiscal Year: 1991
    ..The proposed research will focus on further characterization of this clone by DNA sequence analysis and chromosomal mapping to verify its tentative identification as the embryonic GPDH gene...
  32. Regulation of hemolysin genes in Bacillus
    Michiko Nakano; Fiscal Year: 2007
    ..subtilis by genome mapping and DNA sequence analysis. 2) To characterize the Induction mechanism of the ?-hemolysin gene by the regulatory mutation and by ..
  33. ADENOVIRUS GENOME EXPRESSION: PHYSICAL MAPPING STUDIES
    Clark Tibbetts; Fiscal Year: 1991
    ..b>DNA sequence analysis of the E1A and fiber genes will be performed for representative serotypes of each sub-subgroup to ..
  34. GENETIC ANALYSIS OF TRANSLATION INITIATION IN YEAST
    Michael Hampsey; Fiscal Year: 1993
    ..local (CYC1-linked) from extragenic suppressors; (iii) characterize the CYC1 locus from each by DNA sequence analysis and 5' endpoint transcript mapping; (iv) clone the most appropriate extragenic suppressor of the cycl-362 ..
  35. HUMAN DESMOPLAKIN GENE STRUCTURE & EXPRESSION IN EMBRYOS
    Kathleen Green; Fiscal Year: 1990
    ..the human DP cDNAs (mRNAs) will be determined by restriction mapping, cross- hybridization experiments and DNA sequence analysis. This may allow identification of sequences which could serve as a DPII specific probe...
  36. BIOCHEMISTRY AND GENETICS OF HYPERTENSION
    JOHN RAPP; Fiscal Year: 2002
    ..b>DNA sequence analysis of the candidate alleles involved is then required to find a structural difference that is likely to have ..
  37. STRUCTURE AND EXPRESSION OF MAMMALIAN TUBULIN GENES
    NICHOLAS COWAN; Fiscal Year: 1990
    ..The proposed approach will involve 1) characterization by DNA sequence analysis of human Beta-tubulin genes that encode distinct Beta-tubulin isotypes...
  38. Ex Cyto DNA Sequencing from Single Bacterial Colonies
    David Mead; Fiscal Year: 2006
    ..applicant): Project Summary/Abstract: DNA polymerases are the engines that drive conventional methods of DNA sequence analysis, as well as many of the newer sequencing methods being developed...
  39. SEQUENCING MOUSE GENOMIC CLONES
    Bruce Roe; Fiscal Year: 1999
    ..2. To continue to develop, improve and implement the automated procedures for DNA isolation, DNA sequence analysis, data acquisition, and data analysis, thereby increasing their DNA sequencing efficiency. 3...
  40. GENETIC ANALYSIS OF HEAT SHOCK PROTEIN FUNCTION
    Gregory Phillips; Fiscal Year: 1991
    ..New dnaK and groELS mutants will be characterized by phenotypic comparison with known alleles and by DNA sequence analysis. The ability of DnaK and GroEL to associate with LamB-LacZ hybrid proteins in vivo will also be ..
  41. HEAT SHOCK-LIKE PROTEIN AND CELLULAR DIFFERENTIATION
    John Yu; Fiscal Year: 1990
    ..specifically on the development of immunologic probes with requisite specificity for this protein and its DNA sequence analysis. For immunologic probing of the expression of hemin p70, a panel of monoclonal antibodies with specificity ..
  42. Rim J and thermoregulation of pili transcription
    CHRISTINE WHITE ZIEGLER; Fiscal Year: 2001
    ..Along with the mutational study, DNA sequence analysis will be used to compare RimJ to other N-tenninal acetylases to determine areas of conservation that may ..
  43. ANALYSIS OF E COLI GTP-BINDING PROTEINS AND THEIR GENES
    PAUL MARCH; Fiscal Year: 1993
    ..Interesting mutants will be analyzed phenotypically and by DNA sequence analysis. High level expression vectors will be employed to obtain pure protein (both mutant and wild type) for ..
  44. LIPOOLIGOSACCHARIDE BIOSYNTHESIS IN NEISSERIACEAE
    Daniel Stein; Fiscal Year: 2004
    ..I will characterize these genes by DNA sequence analysis, define the biochemical properties of the gene products and determine their role in the biosynthetic ..
  45. USE OF ILRP AND OFA AS VACCINE IN RODENT TUMOR THERAPY
    Joseph Coggin; Fiscal Year: 2004
    ..identical to an immature form of Laminin Receptor Protein (iLRP approximately equal to OFA) by peptide and DNA sequence analysis. The applicant's three aims are: 1)...
  46. MICROBIAL GENOMICS
    George Weinstock; Fiscal Year: 2001
    ..They have been targeted for DNA sequence analysis by a strategic planning workshop for oral infectious diseases of the NIDCR...
  47. ROLE OF PROTO-ONCOGENES IN THE DEVELOPMENT OF C. ELEGANS
    Mario Capecchi; Fiscal Year: 1990
    ..We are in the process of characterizing candidates for the c-erbB gene. DNA sequence analysis shows that the amino acid sequence of the C...
  48. CONFERENCE--FULFILLING THE PROMISES OF GENOMICS RESEARCH
    Marvin Bayne; Fiscal Year: 2000
    ..Bioinformatics applications to DNA sequence analysis and pattern recognition in mRNA expression arrays will be presented...
  49. Comparative DNA sequence analysis of the yeast genome
    H Johnston; Fiscal Year: 2004
    ..We hope to contribute to the development of comparative DNA sequence analysis as an approach to annotating genomes, and learn how to use it effectively.
  50. MECHANISM IN DOPAMINE RECEPTOR SENSITIVITY REGULATION
    JEANNETTE MILLER; Fiscal Year: 1990
    ..aims of the research include: (A) isolation, positive identification and characterization by complete DNA sequence analysis of cDNAs encoding for mRNAs and their proteins, that may be involved in the development of D2 receptor ..
  51. Enhanced DNA microarray performance with patterned probe
    John Oliver; Fiscal Year: 2005
    ..The objective of the project proposed here is to demonstrate that semi-degenerate bases will function in arrayed, patterned probes as universal bases. ..
  52. Carbon Nanotube Probes for Direct DNA Sequence Analysis
    Charles Lieber; Fiscal Year: 2002
    ..abstract_text> ..
  53. MOLECULAR PHARMACOLOGY OF TUMOR AND VIRUS INHIBITORS
    ARTHUR GROLLMAN; Fiscal Year: 2001
    ..The position of mutations induced is established by DNA sequence analysis. Primer-extension reactions, catalyzed by DNA polymerase, coupled with steady-state kinetic analysis, are ..
  54. Carbon Nanotube Probes for Direct DNA Sequence Analysis
    Charles Lieber; Fiscal Year: 2004
    ..abstract_text> ..
  55. STRUCTURE AND FUNCTION OF PROLINE PERMEASE
    Stanley Maloy; Fiscal Year: 1990
    ..b>DNA sequence analysis of the mutants will identify the amino acid residues that directly interact with the substrate and counter-..
  56. EXPRESSION CLONING COMPONENTS OF THE LPS RECEPTORS
    Sally Orr; Fiscal Year: 2001
    ..Our preliminary results describe the isolation and DNA sequence analysis of a partial murine cDNA (G21) that enables human cells to respond to lipid Iva...
  57. Genetic Regulation of Skeletogenesis
    Yefu Li; Fiscal Year: 2005
    ..To identify Ocd, we plan to examine the coding regions of these genes by direct DNA sequence analysis. 2) To examine the expression profile of Ocd and its down-stream effects on chondrogenesis...
  58. POPULATION BASED INVESTIGATIONS OF TUBERCULOSIS
    David Alland; Fiscal Year: 2004
    ..b>DNA sequence analysis will be combined with classical and molecular epidemiology to study the mutational events that lead to ..
  59. CD8 T CELL MEDIATED SUPPRESSION OF HIV1 FROM INDIA
    Phalguni Gupta; Fiscal Year: 2000
    ..2. To determine the genotypes of HIV-1 present in PBMC from infected subjects from Calcutta by HMA and DNA sequence analysis of the V3-V5 region of the envelope and 3...
  60. MINORITY SCIENTIST AWARD AT MINORITY INSTITUTIONS
    ROMONIA REAMS; Fiscal Year: 1999
    ..nuclear run on assays, reverse-transcriptase polymerase chain reaction, restriction analysis, cloning and DNA sequence analysis. These contemporary approaches in cell and molecular biology will be used by Dr...
  61. CHARACTERIZATION OF NEWLY-IDENTIFIED PROTEIN KINASES
    Steven Hanks; Fiscal Year: 1991
    ..Familial relationships will be confirmed by DNA sequence analysis. Structural and functional information about the putative protein-serine kinases encoded by the clones ..
  62. ANALYSIS OF V CHOLERAE GENES INVOLVED IN COLONIZATION
    KENNETH PETERSON; Fiscal Year: 1993
    ..The four genes encoding Acf determinants will be isolated and subjected to both DNA sequence analysis and computer aided amino acid similarity search...
  63. Natural selection and type 2 diabetes genes
    Vanessa Clark; Fiscal Year: 2006
    ..Previous DNA sequence analysis of CAPN 10 indicates a distinct excess of polymorphism in intron 13...