Showing papers on "Sequence assembly published in 1994"

Automated DNA sequencing and analysis.

Abstract: Sequencing Instruments and Strategies: E. Chen, The Efficiency of Automated DNA Sequencing. G.M. Church, G. Gryan, N. Lakey, S. Kieffer-Higgins, L. Mintz, M. Temple, M. Rubenfield, L. Jaehn, H. Ghazizadel, K. Robison, and P. Richterick, Automated Multiplex Sequencing. X.C. Huang and R.A. Mathies, Application of Capillary Array Electrophoresis to DNA Sequencing. R. Drmanac, S. Drmanac, J. Jarvis, and I. Labat, Sequencing by Hybridization. A. Martin-Gallardo, J. Lamerdin, and A. Carrano, Shotgun Sequencing. A. Bodenteich, S. Chissoe, Y.-F. Wang, and B. Roe, Shotgun Cloning as the Strategy of Choice to Generate Templates for High Throughput Dideoxynucleotide Sequencing. C.M. Berg, G. Wang, K. Isono, H. Kasai, and D.E. Berg, Transposon-Facilitated Large-Scale DNA Sequencing. C.H. Martin, C.A. Mayeda, C.A. Davis, M.P. Strathmann, and M. Palazzolo, Transposon-Facilitated Sequencing: An Effective Set of Procedures to Sequence DNA Fragments Smaller than 4kb. L. Liu and R.D. Fleischmann, Construction of Exonuclease III Nested Deletion Sets for Rapid DNA Sequencing. M. Adams, Expressed Sequence Tags as Tools for Physiology and Genomics. W.R. McCombie, The Use of Automated DNA Sequencing in the Analysis of cDNAs of Model Organisms. Sample Preparation and Sequencing Methods: Libraries: R.L. Stalligs, N.A. Doggett, A. Ford, J. Longmire, C.E. Hildebrand, L.L. Deaven, and R. Moyzis, Applications of Cosmid Libraries in Genome Mapping and Sequencing Efforts. D.A. Smoller, W.J. Kimmerly, O. Hubbard, C. Ericsson, C.H. Martin, and M.J. Palazzolo, A Role for the P1 Cloning System in Genome Analysis. N.A. Doggett, D.L. Grady, J.L. Longmire, and L.L. Deaven, Generation and Mapping of Chromosome Specific Sequence-Tagged Sites (STS). R. Moreno and R. Fuldner, Construction of cDNA Libraries. M.B. Soares, Construction of Directionally Cloned cDNA Libraries and Phagemid Vectors. A. Swaroop, Construction of Directional cDNA Libraries. J.M. Kwak and J.G. Nam, Preparation of cDNA Libraries from Brassica. J.M. Sikela, T.J. Stevens, J.A. Hopkins, A.S. Wilcox, J. Glod, A.S. Khan, and A.K. Orpana, Abundance Screening of Human cDNA Libraries. G. Lennon, High Density Grid Technologies. Automated Sample Preparation: D.R. Sibson, Solid Phrase Preparation of Sequencing Templates from PCR Products. A. Holmberg, G. Fry, and M. Uhlon, Automatic Preparation of DNA Templatesfor Sequencing on the ABI Catalyst Robotic Workstation. T. Hawkins, Custom Magnetic Particles: Their Use in DNA Purification. Sequencing Methods: W.R. McCombie and A. Martin-Gallardo, Large-Scale Automated Sequencing of Human Chromosomal Regions. L. Rowen and B.F. Koop, Zen and the Art of Large-Scale Genomic Sequencing. J.M. Kelley, Automated Dye Terminator DNA Sequencing. D.M. Muzny, S. Richards, Y. Shen, and R.A. Gibbs, PCR Based Strategies for Gap Closure in Large Scale Sequencing Projects. S. Richards, D.M. Muzny, A.B. Civitello, F. Lu, and R.A. Gibbs, Sequence Map Gaps and Directed Reverse Sequencing for the Completion of Large Sequencing Projects. F. Iris, Optimized Methods for Large-Scale Shotgun DNASequencing in Alu-Rich Genomic Regions. S.G. Burgett and P.R. Rosteck, Jr., Use of Dimethylsulfoxide to Improve Fluorescent, Tag Cycle Sequencing. Informatics: Sequence Assembly Theory and Algorithms: C. Tibbetts, J.M. Bowling, and J.B. Golden, III, Neural Networks for Automated Base Calling of Gel Based DNA Sequencing Ladders. G. Myers, Advances in Sequence Assembly. S. Honda, N.W. Parrott, and C.B. Lawrence, Computer Aided Sequence Reconstruction: Software Support for Multiple Large-Scale Sequencing Strategies. C. Burks, M.L. Engle, S. Forrest, R.J. Parsons, C.A. Soderlund, and P.E. Stolorz, Relaxation and Optimization Methods for Sequence Assembly. Data Analysis Tools: G. Sutton and T. Kerlavage, Software Tools for Protein Similarity Searching. J.M. Claverie, Large-Scale Sequence Analysis. J. Shavlik, Finding Frame Shift Errors in Anonymous DNA. B. Rappaport, J. Gatewood, C. Fields, and N. Doggett, Integrating Repeat Identification withThermal Calculations. J. Jurka, Approaches to Identification and Analysis of Interspersed Repetitive DNA Sequences. O. White and T. Dunning, Compositional Properties of Exons and Introns. E.C. Uberbacher, X. Guan, and R.J. Mural, A Practical Guide to the GRAIL Email Server. S. Henikoff, J. Henikoff, S. Agus, and J.C. Wallace, Searching for Homologies to Protein Blocks by Electronic Mail. C. Fields, Integrating Computational and Experimental Methods. Data Management and Databases: S. Lewis, Design Issues in Developing Laboratory Information Management Systems. J. Cuticchia, A Relational Database Primer for Molecular Biologists. J.M. Cherry and S.W. Cartinhour, ACEDB: A Tool for Biological Information. R. Overbeek and M. Price, The Integration of Curated Biological Databases.

Towards DNA Sequencing Chips

Abstract: DNA sequencing is an important technology for the determination of the sequences of nucleotides that make up a given DNA fragment. In view of the limitations of current sequencing technology, it would be advantageous to have a DNA sequencing method that provides the sequences of long DNA fragments and is amenable to automation. Sequencing by Hybridization (SBH) is a challenging alternative to the classical sequencing methods. The basic approach is to build an array (Sequencing Chip) of short DNA fragments of lenght l and to use biochemical methods for finding all substrings of lenght l of an unknown DNA fragment. Combinatorial algorithms are then used to reconstruct the sequence of the fragment from the l-tuple composition. In this article we review biochemical, mathematical, and technological aspects of SBH and present a new sequencing chip design which might allow significant chip miniaturization without loss of the resolution of the method.

Genomic sequence sampling: a strategy for high resolution sequence-based physical mapping of complex genomes.

Abstract: We present a simple and efficient method for constructing high resolution physical maps of large regions of genomic DNA based upon sampled sequencing. The physical map is constructed by ordering high density cosmid contigs and determining a sequence fragment from each end of every clone. The resulting map, which contains 30-50% of the complete DNA sequence, allows the identification of many genes and makes possible PCR amplification of virtually any part of the genome. We apply this strategy to the automated analysis of the genome of the primitive eukaryote Giardia lamblia and evaluate its applicability to the physical mapping and DNA sequencing of the human genome.

Manifold sequencing: efficient processing of large sets of sequencing reactions.

Abstract: Automated instruments for DNA sequencing greatly simplify data collection in the Sanger sequencing procedure By contrast, the so-called front-end problems of preparing sequencing templates, performing sequencing reactions, and loading these on the instruments remain major obstacles to extensive sequencing projects We describe here the use of a manifold support to prepare and perform sequencing reactions on large sets of templates in parallel, as well as to load the reaction products on a sequencing instrument In this manner, all reaction steps are performed without pipetting the samples The strategy is applied to sequencing PCR-amplified clones of the human mitochondrial D-loop and for detection of heterozygous positions in the human major histocompatibility complex class II gene HLA-DQB, amplified from genomic DNA samples This technique will promote sequencing in a clinical context and could form the basis of more efficient genomic sequencing strategies

A quantitative comparison of DNA sequence assembly programs.

Abstract: We have compared 11 sequence assembly programs for the accuracy and reproducibility with which they assemble DNA fragments into a completed sequence. To test the assemblers under controlled conditions, the rat multidrug resistance (RATMDRM) gene sequence was randomly divided into overlapping 200- to 400-base fragments. Various degrees of error, in the form of miss-identified bases, missed bases, and duplicated bases, were randomly added to these fragments. The probability of an error, and the type of error, was modified using an error distribution template that was developed by comparing the original fragments used to sequence RATMDRM with the final, edited sequence stored in GenBank. From 0 to 15% error was then added to independent sets of fragments, and assemblage was attempted. The quality of the assemblages was evaluated by comparing the number of differences between the assembled sequence and the original sequence. Tests were also done to determine if the order in which fragments were added...

Fully-automated, nonradioactive solid-phase sequencing of genomic DNA obtained from PCR.

Abstract: Nonradioactive sequencing in combination with solid-phase template purification is a powerful method for sequence analysis, especially of PCR-generated fragments. To perform DNA sequencing under optimal conditions, it is necessary to obtain a well-purified and single-stranded (ss) DNA template. The disadvantage of ssDNA sequencing is that additional steps are required to generate ssDNA templates before any sequencing reactions can be carried out and is thus more time-consuming. Here we describe an automated solid-phase system for direct sequencing of ssPCR products that incorporates magnetic beads coated with streptavidin as solid support and a computer-controlled device (PolySeq) with heating, magnetic and mixing functions, all of which are integrated into a robotic workstation (Biomek 1000). This solid-phase method is extremely useful for rapid template purification and strand separation of DNA obtained from PCR as well as for high-quality dideoxyribonucleotide chain termination sequencing with fluorescently labeled primers. The system allows the complete automation of the sequencing procedure starting with PCR amplicons. DNA sequencing results obtained with this system were reproducible and gave an excellent length of readable sequences with low background and an analysis capacity of 30,000-40,000 bp per week.

Method for generation of sequence sampled maps of complex genomes

Abstract: The present invention relates to a rapid and powerful sequence "sequence sampled mapping" method for sequencing complex genomes. The invention method is applicable to genomic DNA, preferably mammalian chromosomes, and in a preferred embodiment, employs a "bottom-up" mapping strategy, which allows for the simultaneous analysis of multiple cosmid clones for the detection of overlaps. The sequence sample mapping method is useful first, for the completion of high density sequence-based maps, and ultimately, for the complete sequencing of genomic DNA directly from cosmid clones.

Integration of competing ancillary assertions in genome assembly.

Abstract: Assembly of genomic sequences and maps relies on a primary set of experimental data (e.g., the sequences of individual DNA fragments, or hybridization fingerprints of individual clone inserts), but almost always also relies on several streams of related but distinct kinds of data for completeness and accuracy of the final construction. These secondary data sets, which we term ancillary information, usually contain errors (as do the primary data sets, therefore creating the possibility of conflict between data sets), often arise from different experimental protocols and correspond to different scales of measurement, and occasionally include non-quantitative statements about the data. We present an approach for integration of ancillary assertions in the ow timization of genome assembly, based on simultaneous balancing among the primary and secondary data sets, and include specific examples in the context of assembling DNA sequencing fragments to reconstruct a parent sequence.