Nucleic Acids Research, 1995, Vol. 23, No. 24 4992-4999
© 1995
Articles |
A new DNA sequence assembly program
MRC Laboratory of Molecular Biology Hills Road, Cambridge CB2 2QH, UK
*To whom correspondence should be addressed
Received September 29, 1995. Accepted November 15, 1995.
We describe the Genome Assembly Program (GAP), a new program for DNA sequence assembly. The program is suitable for large and small projects, a variety of strategies and can handle data from a range of sequencing instruments. It retains the useful components of our previous work, but includes many novel Ideas and methods. Many of these methods have been made possible by the program's completely new, and highly interactive, graphical user interface. The program provides many visual clues to the current state of a sequencing project and allows users to interact In intuitive and graphical ways with their data. The program has tools to display and manipulate the various types of data that help to solve and check difficult assemblies, particularly those in repetitive genomes. We have introduced the following new displays: the Contig Selector, the Contlg Comparator, the Template Display, the Restriction Enzyme Map and the Stop Codon Map. We have also made it possible to have any number of Contig Editors and Contig Joining Editors running simultaneously even on the same contig. The program also includes a new ‘Directed Assembly’ algorithm and routines for automatically detecting unfinished segments of sequence, to which it suggests experimental solutions.
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|
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|
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|
|
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|
|
|
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|
|
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|
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|
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|
|
R. J. Daniels, J. F. Peden, C. Lloyd, S. W. Horsley, K. Clark, C. Tufarelli, L. Kearney, V. J. Buckle, N. A. Doggett, J. Flint, et al. Sequence, structure and pathology of the fully annotated terminal 2 Mb of the short arm of human chromosome 16 Hum. Mol. Genet., February 1, 2001; 10(4): 339 - 352. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Janssens, S. Goossens, K. Staes, B. Gilbert, J. van Hengel, C. Colpaert, E. Bruyneel, M. Mareel, and F. van Roy {alpha}T-Catenin: a novel tissue-specific {beta}-catenin-binding protein mediating strong cell-cell adhesion J. Cell Sci., January 9, 2001; 114(17): 3177 - 3188. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Evans, D. Cavanagh, and P. Britton Utilizing fowlpox virus recombinants to generate defective RNAs of the coronavirus infectious bronchitis virus J. Gen. Virol., December 1, 2000; 81(12): 2855 - 2865. [Abstract] [Full Text]
|
|
|
|
 |
|
 D. D. Pollock, J. A. Eisen, N. A. Doggett, and M. P. Cummings A Case for Evolutionary Genomics and the Comprehensive Examination of Sequence Biodiversity Mol. Biol. Evol., December 1, 2000; 17(12): 1776 - 1788. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. A. Whistler, V. O. Stockwell, and J. E. Loper Lon Protease Influences Antibiotic Production and UV Tolerance of Pseudomonas fluorescens Pf-5 Appl. Envir. Microbiol., July 1, 2000; 66(7): 2718 - 2725. [Abstract] [Full Text]
|
|
|
|
|
|
A.-M. Mallon, M. Platzer, R. Bate, G. Gloeckner, M.R.M. Botcherby, G. Nordsiek, M.A. Strivens, P. Kioschis, A. Dangel, D. Cunningham, et al. Comparative Genome Sequence Analysis of the Bpa/Str Region in Mouse and Man Genome Res., June 1, 2000; 10(6): 758 - 775. [Abstract] [Full Text]
|
|
|
|
|
|
A. M. Nedelcu, R. W. Lee, C. Lemieux, M. W. Gray, and G. Burger The Complete Mitochondrial DNA Sequence of Scenedesmus obliquus Reflects an Intermediate Stage in the Evolution of the Green Algal Mitochondrial Genome Genome Res., June 1, 2000; 10(6): 819 - 831. [Abstract] [Full Text]
|
|
|
|
|
|
P. A. Lyons, N. Armitage, F. Argentina, P. Denny, N. J. Hill, C. J. Lord, M. B. Wilusz, L. B. Peterson, L. S. Wicker, and J. A. Todd Congenic Mapping of the Type 1 Diabetes Locus, Idd3, to a 780-kb Region of Mouse Chromosome 3: Identification of a Candidate Segment of Ancestral DNA by Haplotype Mapping Genome Res., April 1, 2000; 10(4): 446 - 453. [Abstract] [Full Text]
|
|
|
|
|
|
B. Silakowski, H. U. Schairer, H. Ehret, B. Kunze, S. Weinig, G. Nordsiek, P. Brandt, H. Blocker, G. Hofle, S. Beyer, et al. New Lessons for Combinatorial Biosynthesis from Myxobacteria. THE MYXOTHIAZOL BIOSYNTHETIC GENE CLUSTER OF Stigmatella aurantiaca DW4/3-1 J. Biol. Chem., December 24, 1999; 274(52): 37391 - 37399. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Frangeul, K. E. Nelson, C. Buchrieser, A. Danchin, P. Glaser, and F. Kunst Cloning and assembly strategies in microbial genome projects Microbiology, October 1, 1999; 145(10): 2625 - 2634. [Full Text] [PDF]
|
|
|
|
|
|
A Alcami, A Khanna, N. Paul, and G. Smith Vaccinia virus strains Lister, USSR and Evans express soluble and cell- surface tumour necrosis factor receptors J. Gen. Virol., April 1, 1999; 80(4): 949 - 959. [Abstract]
|
|
|
|
|
|
S. Haapa, S. Suomalainen, S. Eerikäinen, M. Airaksinen, L. Paulin, and H. Savilahti An Efficient DNA Sequencing Strategy Based on the Bacteriophage Mu in Vitro DNA Transposition Reaction Genome Res., March 1, 1999; 9(3): 308 - 315. [Abstract] [Full Text]
|
|
|
|
|
|
S Bonne, J van Hengel, F Nollet, P Kools, and F van Roy Plakophilin-3, a novel armadillo-like protein present in nuclei and desmosomes of epithelial cells J. Cell Sci., January 7, 1999; 112(14): 2265 - 2276. [Abstract] [PDF]
|
|
|
|
 |
|
 The C. elegans Sequencing Consortium Genome Sequence of the Nematode C. elegans: A Platform for Investigating Biology Science, December 11, 1998; 282(5396): 2012 - 2018. [Abstract] [Full Text]
|
|
|
|
|
|
T. S. Centre and T. W. U. G. S. Center Toward a Complete Human Genome Sequence Genome Res., November 1, 1998; 8(11): 1097 - 1108. [Abstract] [Full Text]
|
|
|
|
|
|
F. Sterky, S. Regan, J. Karlsson, M. Hertzberg, A. Rohde, A. Holmberg, B. Amini, R. Bhalerao, M. Larsson, R. Villarroel, et al. Gene discovery in the wood-forming tissues of poplar: Analysis of 5,692 expressed sequence tags PNAS, October 27, 1998; 95(22): 13330 - 13335. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. C. Wendl, S. Dear, D. Hodgson, and L. Hillier Automated Sequence Preprocessing in a Large-Scale Sequencing Environment Genome Res., September 1, 1998; 8(9): 975 - 984. [Abstract] [Full Text]
|
|
|
|
|
|
P. Taillon-Miller, Z. Gu, Q. Li, L. Hillier, and P.-Y. Kwok Overlapping Genomic Sequences: A Treasure Trove of Single-Nucleotide Polymorphisms Genome Res., July 1, 1998; 8(7): 748 - 754. [Abstract] [Full Text]
|
|
|
|
|
|
D. Gordon, C. Abajian, and P. Green Consed: A Graphical Tool for Sequence Finishing Genome Res., March 1, 1998; 8(3): 195 - 202. [Abstract] [Full Text]
|
|
|
|
|
|
S. Dear, R. Durbin, L. Hillier, G. Marth, J. Thierry-Mieg, and R. Mott Sequence Assembly with CAFTOOLS Genome Res., March 1, 1998; 8(3): 260 - 267. [Abstract] [Full Text]
|
|
|
|
|
|
F. Francis, T. M. Strom, S. Hennig, A. Boddrich, B. Lorenz, O. Brandau, K. L. Mohnike, M. Cagnoli, C. Steffens, S. Klages, et al. Genomic Organization of the Human PEX Gene Mutated in X-Linked Dominant Hypophosphatemic Rickets Genome Res., June 1, 1997; 7(6): 573 - 585. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D Tremousaygue, C Bardet, P Dabos, F Regad, F Pelese, R Nazer, E Gander, and B Lescure Genome DNA sequencing around the EF-1 alpha multigene locus of Arabidopsis thaliana indicates a high gene density and a shuffling of noncoding regions. Genome Res., March 1, 1997; 7(3): 198 - 209. [Abstract] [PDF]
|
|
|
|
|
|
K Kawasaki, S Minoshima, E Nakato, K Shibuya, A Shintani, J L Schmeits, J Wang, and N Shimizu One-megabase sequence analysis of the human immunoglobulin lambda gene locus. Genome Res., March 1, 1997; 7(3): 250 - 261. [Abstract] [PDF]
|
|
|
|
|
|
M. R. Ehrenstein, C. Rada, A.-M. Jones, C. Milstein, and M. S. Neuberger Switch junction sequences in PMS2-deficient mice reveal a microhomology-mediated mechanism of Ig class switch recombination PNAS, December 4, 2001; 98(25): 14553 - 14558. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. J. Kent and D. Haussler Assembly of the Working Draft of the Human Genome with GigAssembler Genome Res., September 1, 2001; 11(9): 1541 - 1548. [Abstract] [Full Text] [PDF]
|
|