E.B. Lewis, J.D. Knafels, D.R. Mathog, and S.E. Celniker (1995). Sequence analysis of the cis-regulatory regions of the bithorax complex of Drosophila. Proc. Natl. Acad. Sci. USA 92:8403-8407.
bioTkperl: G. Helt (1997). Data visualization and gene discovery in Drosophila melanogaster. PhD thesis, University of California at Berkeley.
bioTk: D.B. Searls (1995). bioTk: Componentry for genome informatics graphical user interfaces. COMBIS. http://www.cbil.upenn.edu/~dsearls/bioTk_paper/paper.html
h78_1_c10: Collins, C., and T. Cloutier (unpublished). Annotations on sequence h78_1_c10. Personal communication.
Standardized gene set:
D. Kulp, D. Haussler, M.G. Reese, and F.H. Eeckman (1996). A generalized hidden Markov
model for the recognition of human genes in DNA. Proc. Conf. on Intelligent Systems in
Molecular Biology '96, St. Louis, Missouri, AAAI/MIT Press.
Set of 305 genes is available at ftp://www-hgc.lbl.gov/pub/genesets.
ACeDB: R. Durbin and J. Thierry-Mieg (1991-). A C. elegans Database. Documentation, code and data available from anonymous FTP servers at lirmm.lirmm.fr, cele.mrc-lmb.cam.ac.uk and ncbi.nlm.nih.gov.
BLAST: S.F. Altschul, W. Gish, W. Miller, E.W. Myers, and D.J. Lipman (1990). Basic local alignment search tool. J. Mol. Biol. 215:403-10.
xblast: J.M. Claverie and D.J. States (1993). Information enhancement methods for large scale sequence analysis. Computers and Chemistry 17:191-201.
GeneFinder: P. Green (1994). Ancient conserved regions in gene sequences. Current Opinions in Structural Biology, 4:404-412.
GRAIL: Y. Xu, R.J. Mural, M.B. Shah and E.C. Uberbacher (1994). Recognizing Exons in Genomic Sequence Using GRAIL II. Genetic Engineering: Principles and Methods, Jane Setlow (ed.), Plenum Press, Vol. 15.
xpound: A. Thomas and M.H. Skolnick (1994). A probabilistic model for detecting coding regions in DNA sequences. IMA Journal of Mathematics Applied in Medicine and Biology, 11:149-160.
GENSCAN: C. Burge and S. Karlin (1997). Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268:78-94.
GenBank: Benson, D.A., Boguski, M.S., Lipman, D.J., Ostell, J., and Ouellette, B.F. (1998). GenBank. Nucleic Acids Res. 26(1), 1-7.
humtfpb: N. Mackman, J.H. Morrissey, B. Fowler and T.S. Edgington (1989). Complete sequence of the human tissue factor gene, a highly regulated cellular receptor that initiates the coagulation protease cascade. Biochemistry 28 (4), 1755-1762.
Genie: D. Kulp, D. Haussler, M.G. Reese and F.H. Eeckman (1996). A generalized hidden Markov model for the recognition of human genes in DNA, Proc. Conf. on Intelligent Systems in Molecular Biology '96, St. Louis, Missouri, AAAI/MIT Press.
NNPP:
M.G. Reese and F.H. Eeckman (1994).
New neural network algorithms for improved eukaryotic promoter site recognition.
The Seventh International Genome Sequencing and Analysis Conference,
Hilton Head Island, South Carolina, September 16-20, 1995.
Splice site prediction: M.G. Reese, F.H. Eeckman, D. Kulp, D. Haussler (1997). Improved splice site detection in Genie. RECOMB (First Annual International Conference on Computational Molecular Biology, 1997), Santa Fe, ed. M. Waterman.
Primer3: S. Rozen and H.J. Skaletsky (1996). Primer3. Code available at http://www-genome.wi.mit.edu/genome_software/other/primer3.html
MSPcrunch and Blixem: E.L.L. Sonnhammer and R. Durbin (1994). A workbench for large scale sequence homology analysis. Comput. Applic. Biosci. 10:301-307.
GeneNomi: N.L. Harris, M.G. Reese, G.A. Helt, and F.H. Eeckman (1996). Towards automatic recognition of exons. Intelligent Systems for Molecular Biology '96, St. Louis, Missouri. [Poster]
Java bioWidgets: G.A. Helt, S. Lewis, A.E. Loraine, and G.M. Rubin (1998). BioViews: Java-based tools for genomic data visualization. http://www.fruitfly.org/publications/bioviews.html
Web page by Nomi Harris (nlharris@lbl.gov)