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Volume 40, Number 2, 2001
Deep computing for the life sciences
 Table of contents: arrowHTML arrowPDF arrowASCII   This article: arrowHTML arrowPDF arrowASCII arrowCopyright info
   

A high-throughput distributed DNA sequence analysis and database system - References
by J. T. Inman, H. R. Flores, G. D. May, J. W. Weller, and C. J. Bell

Cited references and notes

  1. D. R. Walker and E. V. Koonin, “SEALS: A System for Easy Analysis of Lots of Sequences,” Intelligent Systems for Molecular Biology 5, 333–339 (1997).
  2. See http://www.ncbi.nlm.nih.gov/CBBresearch/Walker/SEALS/index.html.
  3. See http://stein.cshl.org/software/boulder/.
  4. M. D. Adams, J. M. Kelley, J. D. Gocayne, M. Dubnick, M. H. Polymeropoulos, H. Xiao, C. R. Merril, A. Wu, B. Olde, R. F. Moreno, A. R. Kerlavage, W. R. McCombie, and J. C. Ventner, “Complementary DNA Sequencing: Expressed Sequence Tags and Human Genome Project,” Science 252, 1651–1656 (1991).
  5. B. Ewing and P. Green, “Base-Calling of Automated Sequencer Traces Using PHRED: II. Error Probabilities,” Genome Research 8, No. 3, 186–194 (1998).
  6. D. Gordon, C. Abajian, and P. Green, “Consed: A Graphical Tool for Sequence Finishing,” Genome Research 8, No. 3, 195–202 (1998).
  7. See http://www.phrap.org.
  8. See http://www.noble.org/medicago/index.htm.
  9. M. Waugh, P. Hraber, J. Weller, Y. Wu, G. Chen, J. Inman, D. Kiphart, and B. Sobral, “The Phytophthora Genome Initiative Database: Informatics and Analysis for Distributed Pathogenomic Research,” Nucleic Acids Research 28, 87–90 (2000).
  10. GenBank is the National Institutes of Health (NIH) genetic sequence database. It is the de facto official public repository of the United States for all of the nucleic acid sequences and is administered by the National Center for Biotechnology Information (NCBI), a branch of the National Library of Medicine.
  11. S. F. Altschul, T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman, “Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs,” Nucleic Acids Research 25, 3389–3402 (1997).
  12. See http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?db=Protein.
  13. The Common Object Request Broker: Architecture and Specification, Revision 2.1, The Object Management Group, Inc., 492 Old Connecticut Path, Framingham, MA (1997).
  14. R. H. Halstead, “MULTILISP: A Language for Concurrent Symbolic Computation,” ACM Transactions on Programming Languages and Systems 7, No. 4, 501–538 (1985).
  15. The “NR” library is a nonredundant database of all known protein sequences. It is derived in part from GenBank and, like GenBank, is maintained by NCBI.
  16. PHP is a server-side, cross-platform, HTML-embedded scripting language with database connectivity capabilities. Its use simplifies the creation of dynamic Web page content.
  17. G. G. Sutton, O. White, M. D. Adams, and A. R. Kerlavage, “TIGR Assembler: A New Tool for Assembling Large Shotgun Sequencing Projects,” Genome Science and Technology 1, 9–19 (1995).
  18. J. Burke, D. Davison, and W. Hide, “d2_cluster: A Validated Method for Clustering EST and Full-Length cDNA Sequences,” Genome Research 9, No. 11, 1135–1142 (1999).
  19. See http://www.sanbi.ac.za.
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