1887

Section 8 : Internet- and Computer-Assisted Gene Analysis

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Abstract:

This section discusses Internet- and computer-assisted gene analysis. Many DNA and protein sequence databases are readily available through the World Wide Web. Important gateway websites, containing links to sequence databases and computational centers for sequence analysis, include the National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EBI), and Pedro's BioMolecular Research Tools (Pedro's). GenBank is a sequence database maintained by the NCBI, the National Library of Medicine, and the National Institutes of Health. Webcutter is a set of restriction enzyme analysis tools on the World Wide Web that can predict restriction enzyme cut sites. The section describes the use of Webcutter to generate a restriction enzyme map of a DNA sequence, and a basic local alignment search tool (BLAST) search for homologous sequences. It also describes the use of the ExPASy server to translate DNA sequence into amino acid sequence. Oligonucleotides are short synthetic fragments of DNA. Oligonucleotides are important components of a polymerase chain reaction (PCR) because they identify the DNA fragment to be amplified. Oligonucleotide length, base composition, and nucleotide sequence affect annealing temperature and function. In addition, the section explains the calculation of the melting temperature (T) of an oligonucleotide, factors that affect oligonucleotide binding and function, and describes primers with computer analysis assistance available on the World Wide Web.

Citation: Scheppler J, Cassin P, Gambier R. 2000. Internet- and Computer-Assisted Gene Analysis, p 225-249. In Biotechnology Explorations. ASM Press, Washington, DC. doi: 10.1128/9781555818135.ch8

Key Concept Ranking

Human immunodeficiency virus 1
0.5014075
0.5014075
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of Figure 25.1
Figure 25.1

NCBI home page.

Citation: Scheppler J, Cassin P, Gambier R. 2000. Internet- and Computer-Assisted Gene Analysis, p 225-249. In Biotechnology Explorations. ASM Press, Washington, DC. doi: 10.1128/9781555818135.ch8
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 25.2
Figure 25.2

GenBank modified search page.

Citation: Scheppler J, Cassin P, Gambier R. 2000. Internet- and Computer-Assisted Gene Analysis, p 225-249. In Biotechnology Explorations. ASM Press, Washington, DC. doi: 10.1128/9781555818135.ch8
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 25.3
Figure 25.3

Entrez nucleotide search page.

Citation: Scheppler J, Cassin P, Gambier R. 2000. Internet- and Computer-Assisted Gene Analysis, p 225-249. In Biotechnology Explorations. ASM Press, Washington, DC. doi: 10.1128/9781555818135.ch8
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 25.4
Figure 25.4

Entrez protein search page.

Citation: Scheppler J, Cassin P, Gambier R. 2000. Internet- and Computer-Assisted Gene Analysis, p 225-249. In Biotechnology Explorations. ASM Press, Washington, DC. doi: 10.1128/9781555818135.ch8
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 26.1
Figure 26.1

Webcutter home page.

Citation: Scheppler J, Cassin P, Gambier R. 2000. Internet- and Computer-Assisted Gene Analysis, p 225-249. In Biotechnology Explorations. ASM Press, Washington, DC. doi: 10.1128/9781555818135.ch8
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 26.2
Figure 26.2

Webcutter restriction enzyme analysis page.

Citation: Scheppler J, Cassin P, Gambier R. 2000. Internet- and Computer-Assisted Gene Analysis, p 225-249. In Biotechnology Explorations. ASM Press, Washington, DC. doi: 10.1128/9781555818135.ch8
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 26.3
Figure 26.3

NCBI BLAST search Web page.

Citation: Scheppler J, Cassin P, Gambier R. 2000. Internet- and Computer-Assisted Gene Analysis, p 225-249. In Biotechnology Explorations. ASM Press, Washington, DC. doi: 10.1128/9781555818135.ch8
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 26.4
Figure 26.4

ExPASy translation analysis Web page.

Citation: Scheppler J, Cassin P, Gambier R. 2000. Internet- and Computer-Assisted Gene Analysis, p 225-249. In Biotechnology Explorations. ASM Press, Washington, DC. doi: 10.1128/9781555818135.ch8
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 27.1
Figure 27.1

Primer design from “ for the world wide web.”

Citation: Scheppler J, Cassin P, Gambier R. 2000. Internet- and Computer-Assisted Gene Analysis, p 225-249. In Biotechnology Explorations. ASM Press, Washington, DC. doi: 10.1128/9781555818135.ch8
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 27.2
Figure 27.2

Results obtained from a limited primer design scheme.

Citation: Scheppler J, Cassin P, Gambier R. 2000. Internet- and Computer-Assisted Gene Analysis, p 225-249. In Biotechnology Explorations. ASM Press, Washington, DC. doi: 10.1128/9781555818135.ch8
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 27.3
Figure 27.3

Primer analysis obtained with D1 S80 locus primers.

Citation: Scheppler J, Cassin P, Gambier R. 2000. Internet- and Computer-Assisted Gene Analysis, p 225-249. In Biotechnology Explorations. ASM Press, Washington, DC. doi: 10.1128/9781555818135.ch8
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555818135.chap8
1. Gelbart, W. M. 1998. Databases in genomic research. Science 282: 659 661.
2. Gershon, D. 1997. Bioinformatics in a post-genomics age. Nature 389: 417 418.
3. Rogers, R. S. 1998. Bioinformatics begins to buzz. Chem. Eng. News 76: 29 33.
4. Sobral, B. W. S. 1997. Common language of bioinformatics. Nature 389: 418 420.
5. Altschul, S. R.,, W. Gish,, W. Miller,, E. W. Myers,, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403 410.
6. Appel, R. D.,, A. Barroch,, and D. F. Hochstrasser. 1994. A new generation of information retrieval tools: the example of the ExPASy WWW server. Trends Biochem. Sci. 19: 258 260.
7. Baxevanis, A. D.,, M. S. Boguski,, and B. F. F. Ouellette,. 1996. Computational analysis of DNA and protein sequences. In B. Birren,, E. D. Green,, S. Klapholz,, R. M. Myers,, and J. Roskams (ed.), Genome Analysis: A Laboratory Manual, vol. 1. Analyzing DNA. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (http://cliol .cshl.org:80/ books/chapters/analdna/gal _chap.htm).
8. Brawley, S. H. 1999. Submission and retrieval of an aligned set of nucleic acid sequences. J. Phycol. 35: 433 437.
9. Bult, C. J. 1998. How to make sense of sequences. Science 282: 635 636.
10. Glick, B. R.,, and J. J. Pasternak. 1998. Molecular Biotechnology: Principles and Applications of Recombinant DNA, 2nd ed. ASM Press, Washington, D.C.
11. Innis, M. A.,, D. H. Gelfand,, J. J. Sninsky,, and T. J. White. 1990. PCR Protocols: a Guide to Methods and Applications. Academic Press, New York, N.Y.
12. Oh, C.-Y.,, S. Kwok,, S. W. Mitchell,, D. H. Mack,, J. J. Sninsky,, J. W. Krebs,, P. Feorino,, D. Warfield,, and G. Schochetman. 1988. DNA amplification for direct detection of HIV-1 in DNA of peripheral blood mononuclear cells. Science 238: 295 297.
13. Prescott, L. M.,, J. P. Harley,, and D. A. Klein. 1996. Microbiology, 3rd ed. William C. Brown Publishers, Dubuque, Iowa.
14. Turner, P. C.,, A. G. McLennan,, A. D. Bates,, and M. R. H. White. 1997. Instant Notes in Molecular Biology. BIOS Scientific Publishers, Springer-Verlag, New York, N.Y.
15. Watson, J. D.,, M. Gilman,, J. Witkowski,, and M. Zoller. 1992. Recombinant DNA, 2nd ed. W. H. Freeman & Co., New York, N.Y.

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error