Molecular Biology Computing References 

Thanks to Fran Lewitter


1. Altschul, S., et al., Basic Local Alignment Search Tool. Journal of Molecular Biology, 1990. 215: p. 403-410.

2. Altschul, S.F., et al., Issues in searching molecular sequence databases. Nature Genetics, 1994. 6(February): p. 119-129.

3. Altschul, S., et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 1997. 25(17): p. 3389-3402.

4. Appel, R., A. Bairoch, and D. Hochstrasser, A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server. Trends in Biochemical Sciences, 1994. 19: p. 258-260.

5. Berger, B., et al., Predicting coiled coils by use of pairwise residue correlations. Proc Natl Acad Sci U S A, 1995. 92(18): p. 8259-63.

6. Fickett, J.W., Finding genes by computer: the state of the art. Trends Genet, 1996. 12(8): p. 316-20.

7. Gish, W. and D.J. States , Identification of protein coding regions by database similarity search. Nature Genetic, 1993. 3: p. 266-72.

8. Goodman, L., More BLAST for the buck. Genome Res, 1997. 7(9): p. 858-9.

9. Henikoff, S. and J. Henikoff, Amino acid substitution matrices from protein blocks. Proceedings of the National Academy of Sciences, 1992. 89: p. 10915-10919.

10. Henikoff, S., Sequence analysis by electronic mail server. TIBS, 1993. 18(July): p. 267-268.

11. Henikoff, J.G., S. Pietrokovski, and S. Henikoff, Recent enhancements to the Blocks Database servers. Nucleic Acids Res, 1997. 25(1): p. 222-5.

12. Higgins, D.G., J.D. Thompson, and T.J. Gibson, Using CLUSTAL for multiple sequence alignments, in Methods Enzymol. 1996, p. 383-402.

13. Hogue, C.W., Cn3D: a new generation of three-dimensional molecular structure viewer. Trends Biochem Sci, 1997. 22(8): p. 314-6.

14. Jaeger, J., D. Turner, and M. Zuker, Predicting Optimal and Suboptimal Secondary Structure for RNA, in Methods in Enzymology. 1990, Academic Press, Inc.: p. 281-306.

15. Lawrence, C., et al., Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment. Science, 1993. 262(8 October 1993): p. 208-214.

16. Lewitter, F., How to limit your sequence search by organism. Trends Genet, 1997. 13(7): p. 286-7.

17. Ouellette, B.F.F. and M.S. Boguski, Database Divisions and Homology Search Files: A Guide for the Perplexed. Genome Res, 1997. 7(10): p. 952-5.

18. Pearson, W. and D. Lipman, Improved tools for biological sequence comparison. Proceedings of the National Academy of Sciences, 1988. 85: p. 2444-2448.

19. Rechsteiner, M. and S.W. Rogers, PEST sequences and regulation by proteolysis. Trends Biochem Sci, 1996. 21(7): p. 267-71.

20. Schuler, G., S. Altschul, and D. Lipman, A Workbench for Multiple Alignment Construction and Analysis. PROTEINS: Structure, Function, and Genetics, 1991. 9: p. 180-190.

21. Smith, R.F., et al., BCM Search Launcher--an integrated interface to molecular biology data base search and analysis services available on the World Wide Web. Genome Res, 1996. 6(5): p. 454-62.

22. Uberbacher, E. and R. Mural, Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach. Proceedings of the National Academy of Sciences, 1991. 88: p. 11261-11265.

23. Wolf, E., P.S. Kim, and B. Berger, MultiCoil: a program for predicting two- and three-stranded coiled coils. Protein Sci, 1997. 6(6): p. 1179-89.

24. Worley, K.C., B.A. Wiese, and R.F. Smith, BEAUTY: an enhanced BLAST-based search tool that integrates multiple biological information resources into sequence similarity search results. Genome Res, 1995. 5(2): p. 173-84.

25. Zhang, J. and T. Madden, PowerBLAST: A New Network BLAST Application for Interactive or Automated Sequence Analysis and Annotation. Genome Research, 1997. 7(6): p. 649-656.

26. Zuker, M., On Finding All Suboptimal Foldings of an RNA Molecule. Science, 1989. 244: p. 48-52.

27. Zuker, M., J. Jaeger, and D. Turner, A comparison of optimal and suboptimal RNA secondary structures predicted by free energy minimization with structures determined by phylogenetic comparison. Nucleic Acids Research, 1991. 19(10): p. 2707-2714.


Maintained by Fran Lewitter (11/97)

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