References

[1] NIH working definition of bioinformatics and computational biology. http://www.bisti.nih.gov/CompuBioDef.pdf. 2000

[2] Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. JMolBiol 1990;215:403-10

[3] Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25: 3389-402

[4] Gish W. WU BLAST, http://blast.wustl.edu. 1996-2003

[5] Ma B, Tromp J, Li M. PatternHunter: faster and more sensitive homology search. Bioinformatics 2002; 18:440-5

[6] Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res 2003; 13:103-7

[7] Needleman SB, Wunsch CD. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 1970;48:443-53

[8] Smith TF, Waterman MS. Identification of common molecular subsequences. JMolBiol 1981; 147:195-7

[9] Huang XQ, Miller W. A time-efficient, linear-space local similarity algorithm. AdvApplMath 1991; 12:337-57

[10] Zhang Z, Schwartz S, Wagner L, Miller W. A greedy algorithm for aligning DNA sequences. J Comput Biol 2000; 7:203-14

[11] Ning Z, Cox AJ, Mullikin JC. SSAHA: a fast search method for large DNA databases. Genome Res 2001; 11: 1725-9

[12] Kent WJ. BLAT-the BLAST-like alignment tool. Genome Res 2002; 12: 656-64

[13] Solovyev V, Kolchanov N. Search for functional sites using consensus. In Kolchanov NA and Lim HA (Editors): Computer analysis of genetic macromolecules. Structure, function and evolution, World Scientific, 1999; 183:16-21

[14] Zhang MQ, Marr TG. A weight array method for splicing signal analysis. Comput Appl Biosci 1993;9:499-509

[15] Xu Y, Einstein JR, Mural RJ, Shah M, Uberbacher EC. An improved system for exon recognition and gene modeling in human DNA sequences. In Proceedings of the 2nd International Conference Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, 1994; pp. 376-84

[16] B├╝rge C, Karlin S. Prediction of complete gene structures in human genomic DNA. J Mol Biol 1997; 268: 78-94

[17] Rust AG, Mongin E, Birney E. Genome annotation techniques: new approaches and challenges. Drug Discov Today 2002; 7: S70-6

[18] Chou PY, Fasman GD. Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. Biochemistry 1974; 13:211-22

[19] McGuffm LJ, Bryson K, Jones DT. The PSIPRED protein structure prediction server. Bioinformatics 2000; 16:404-5

[20] Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE. A geometric approach to macromolecule-ligand interactions. J Mol Biol 1982; 161: 269-88

[21] Jones G Willett P, Glen RC. Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J Mol Biol 1995; 245:43-53

[22] Mangoni M, Roccatano D, Di Nola A. Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation. Proteins 1999;35:153-62

[23] Goodsell DS, Morris GM, Olson AJ. Automated docking of flexible ligands: applications of Autodock. J Mol Recog 1996; 9:1-5

[24] Gautheret D, Poirot O, Lopez F, Audic S, Claverie JM. Alternate polyadenylation in human mRNAs: a large-scale analysis by EST clustering. Genome Res 1998; 8: 524-30

[25] Quackenbush J, Liang F, Holt I, Pertea G Upton J. The TIGR gene indices: reconstruction and representation of expressed gene sequences. Nucleic Acids Res 2000; 28:141-5

[26] Eddy SR. Profile hidden Markov models. Bioinformatics 1998; 14:755-63

[27] Huang X, Madan A. CAP3: A DNA sequence assembly program. Genome Res 1999; 9:868-77

[28] G SQ White O, Adams MD, Kerlavage AR. TIGR Assembler: a new tool for assembling large shotgun sequencing projects. Genome Sei Tech 1995; 1: 1-9

[29] Chen T, Skiena SS. A case study in genome-level fragment assembly. Bioinformatics 2000; 16:494-500

[30] Flicek P, Keibler E, Hu P, Korf I, Brent MR. Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map. Genome Res 2003; 13:46-54

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