Bibliographie du cours de Bioinformatique

Altschul S. F., Gish W., Miller W., Myers E. W. and Lipman D. J. (1990). Basic local alignment search tool. J. Mol. Biol., 215, 403-410.

Altschul S. F. (1991). Amino acid substitution matrices from an information theoretic perspective. J. Mol. Biol., 219, 555-565.

Altschul S. F., Boguski M. S., Gish W. and Wootton C. (1994). Issues in searching molecular sequence databases. Nature Genetics, 6, 119-129.

Argos P. (1987). A sensitive procedure to compare amino acid sequences. J. Mol. Biol., 193 385-396.

Argos P. and Vigron M. (1990). Sensitivity comparison of protein amino acid sequences. Methods Enzymol., 183, 352-365.

Bairoch A. and Boeckmann B. (1993). The SWISS-PROT protein sequence data bank, recent developments. Nucleic Acids Res., 21, 3093-3096.

Bairoch A. (1993). The PROSITE dictionary of sites and patterns in proteins, its current status. Nucleic Acids Res., 21, 3097-3103.

Bairoch A. and Boeckmann B. (1994). The SWISS-PROT protein sequence data bank: current status. Nucleic Acids Res., 22, 3578-3580.

Bairoch A. and Bucher P. (1994). PROSITE: recent developments. Nucleic Acids Res., 22, 3583-3589.

Benner S. A., Cohen M. A. and Gonnet G. H. (1994). Amino acid substitution during functionally constrained divergent evolution of protein sequences. Protein Eng., 7, 1323-1332.

Bilofsky H. S., Burks C., Fickett J. W., Goad W. B., Lewitter F. I., Rindone W. P., Swindell C. D. and Tung C. S. (1986). The GenBank genetic sequence databank. Nucleic Acids Res., 14, 1-4.

Bishop M. J. , Ginsburg M. , Rawlings C.J., Wakeford R. (1987). Molecular sequence databases. In Nucleic acid and protein sequence analysis, a practical approach. IRL Press. 83-113.

Brutlag D., Dautricourt J.P., Maulik S., and Relph J. (1990). Improved sensitivity of biological sequence database searches. Comput. Appl. Biosci., 6, 237-245.

Bucher P. (1990). Weight matrix descriptions of four eukaryotic RNA polymerase II promoter derived from 502 unrelated promoter sequences. J. Mol. Biol., 212, 563-578.

Cameron G. N. and Hamm G. H. (1986). The EMBL data library. Nucleic Acids Res., 14, 5-9.

Califano A. and Rigoutsos I. (1993). FLASH: Fast look-up algorithm for string homology. ISMB, 1, 56-64.

Carrez C. (1990) Des structures aux bases de données. Dunod informatique, Paris.

Chen Q. K., Hertz G. Z. and Stormo G.D. (1995). MATRIX SEARCH 1.0; A computer program that scans DNA sequences for transcriptional elements using a database of weight matrices. Comput. Appl. Biosci., 11, 563-566.

Claverie J. M. and States D. J. (1993). Information enhancement methods for large scale sequence sequence analysis. Computers in Chemistry, 17, 191-201.

Cockwell K. Y. and Giles I. G. (1989). Software tools for motif and pattern scanning: program descriptions including a universal sequence reading algorithm. Comput. Appl. Biosci., 5, 227-232.

Collins J. F. and Coulson A. F. (1987). Molecular sequence comparison and alignment. In Nucleic acid and protein sequence analysis, a practical approach. IRL Press. 323-358.

Collins J. F., Coulson A. F. and Lyall A. (1988). The significance of protein sequence similarities. Comput. Appl. Biosci., 4, 67-71.

Collins J. F. and Coulson A. F. (1990). Significance of protein sequence similarities. Methods Enzymol., 183, 474-487.

Creighton T. E. (1984). Disulfide bond formation in proteins. Methods Enzymol., 118, 305-329.

Danchin A., Medigue C., Gascuel O., Soldano H. and Henaut A. (1991). From data banks to data bases. Res. Microbiol., 142, 913-916.

Dang V. D., Valens M., Bolotin-Fukuhara M. and Daignan-Fornier B. (1994). A genetic screen to isolate genes regulated by the yeast CCAAT-box binding protein Hap2p. Yeast, 10, 1273-1283.

Dang V. D., Bohn C., Bolotin-Fukuhara M. and Daignan-Fornier B. (1995). The HAP complex: A general factor regulating energy metabolism yeast.

Darmerval T. et Dessen P. (1992). Banques de données en biologie moléculaire. Biofutur, 53, 3-11.

Dayhoff M. O., Schwartz R. M. and Orcutt B. C. (1978). A model of evolutionary change in proteins. Atlas of Protein Structure, 5, Suppl. 3, 345-352.

Dessen P., Fondrat C., Valencien C. and Mugnier C. (1990) BISANCE: a French service for access to biomolecule sequence databases. Comput. Appl. Biosci., 6, 355-356.

Devereux J., Haeberli P. and Smithies O. (1984). A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res., 12, 387-395.

Doolittle R. F. (1981). Similar amino acid sequences: chance or common ancestry? Science, 214, 149-159.

Doolittle R. F. (1986). OF URFS AND ORFS: A primer on how to analyse derived amino acid sequence. University Sciences Books, 103 pages.

Doolittle R. F. (1990). Searching through sequence databases. Methods Enzymol., 183, 99-110.

Dumas J. P. and Ninio J. (1982). Efficient algorithms for folding and comparing nucleic acid sequences. Nucleic Acids Res., 10, 197-206.

Duret L., Mouchiroud D. and Gouy M. (1994). HOVERGEN: a database of homologous vertebrate genes. Nucleic Acids Res., 22, 2360-2365.

Etzold T. and Argos P. (1993). SRS - an indexing and retrieval tool for flat file data libraries. Comput. Appl. Biosci., 9, 49-57.

Feng D. F., Johnson M. S. and Doolittle R.F. (1985). Aligning amino acid sequences: comparison of commonly used methods. J. Mol. Evol., 21, 112-125.

Fitch W. M. (1966) An improved method of testing for evolutionary homology. J. Mol. Biol., 16, 9-16.

Fondrat C. and Kalogeropoulos A. (1994). Approaching the function of new genes by detection of their potential upstream activation sequences in Saccharomyces cerevisiae: application to chromosome III. Curr. Genet., 25, 396-406.

Fondrat C. and Dessen P. (1995). A rapid access motif database (RAMdb) with a search algorithm for the retrieval patterns in nucleic acids or protein databanks Comput. Appl. Biosci., 11, 273-279.

Forsburg S. L. and Guarente L. (1989). Identification and characterization of HAP4: a third component of the CCAAT-bound HAP2/HAP3 heteromer. Genes Dev., 3, 1166-1178.

Fuchs R. (1993). Block searches on VAX and Alpha computer systems. Comput. Appl. Biosci., 9, 587-591.

Gautier C., Gouy M., Jacobzone M. and Grantham R. (1981). Nucleic acid sequences handbook. Praeger Publishers, London.

George D. G., Barker W.C., and Hunt L.T. (1986). The protein identification resource (PIR). Nucleic Acids Res., 14, 11-15.

George D. G., Barker W.C., and Hunt L.T. (1990). Mutation data matrix and its uses. Methods Enzymol., 183, 333-351.

Ghosh D. (1993). Status of the transcription factors database (TFD). Nucleic Acids Res., 21, 3117-3118.

Ginsburg M. (1987). On line services. In Nucleic acid and protein sequence analysis, a practical approach. IRL Press. 83-113.

Goad W. B. and Kanehisa M. I. (1982). Pattern recognition in nucleic acid sequences. I. A general method for finding local homologies and symmetries. Nucleic Acids Res., 10, 247-263.

Gonnet G. H., Cohen M. A. and Benner S. A. (1992) Exhaustive matching of the entire protein sequence database. Science, 256, 1443-1444.

Gouy M., Gautier C., Attimonelli M., Lanave C., and di Paola G. (1985). ACNUC - a portable retrieval system for nucleic acid sequence databases : logical and physical designs and usage. Comput. Appl. Biosci., 1, 167-172.

Gribskov M., McLachlan A. D. and Eisenberg D. (1987). Profile analysis: detection of distantly related proteins. Proc. Natl. Acad. Sci. USA, 84, 4355-4358.

Gribskov M., Luthy R. and Eisenberg D. (1990). Profile analysis. Methods Enzymol., 183, 146-159.

Hamm G.H. and Cameron G.N. (1986). The EMBL data library. Nucleic Acids Res., 19, 5-9.

Henikoff S. and Henikoff J. G. (1991). Automated assembly of protein blocks for database searching. Nucleic Acids Res., 19, 6565-6572.

Henikoff S. and Henikoff J. G. (1992). Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA, 89, 10915-10919.

Henikoff S. and Henikoff J. G. (1993). Performance evaluation of amino acid substitution matrices. Proteins: Struct. Funct. Genet., 17, 49-61.

Higgins D. G. and Sharp P. M. (1989). Fast and sensitive multiple algnments on a microcomputer. Comput. Appl. Biosci., 5, 151-153.

Johnson M. S. and Overington J. P. (1993). A structural basis for sequence comparisons. An evaluation of scoring methodologies. J. Mol. Biol., 233, 716-738.

Jones D. T., Taylor W. R. and Thornton J. M. (1992). The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci., 8, 275-282.

Kalogeropoulos A. (1993). Linguistic analysis of chromosome III DNA sequence of Saccharomyces cerevisiae. Yeast, 9, 889-905.

Kalogeropoulos A. (1995). Automatic intron detection in nuclear DNA sequences of Saccharomyces cerevisiae. Yeast, 11, 555-565.

Kamech N., Fondrat C., Akli S. and Szajnert M.-F. (1993). PcrBase: un logiciel d'aide à la PCR en interface avec les banques de séquences nucléïques. Medecine-Sciences, 9, 1256-1261.

Karlin S. and Altschul S. F. (1990). Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc Natl Acad Sci USA, 87, 2264-2268.

Karlin S. and Altschul S. F. (1993). Applications and statistics for multiple high-scoring segments in molecular sequences. Proc. Natl. Acad. Sci. USA, 90, 5873-5877.

Keen G., Redgrave G., Lawton J., Linkosky M., Mishra S., Fickett J. and Burks C. (1992). Access to molecular biology databases. 16, 93-101.

Keil B. (1990) Cooperation between databases and scientific community. Methods Enzymol., 183, 50-60.

Kröger M., Wahl R. and Rice P. (1991). Compilation of DNA sequences of Escherichia coli (update 1991). Nucleic Acids Res., 19 Suppl., 2023-2043.

Knüppel R., Dietze P., Lehnberg W., Frech K., Wingender E. (1994). TRANSFAC Retrieval Program: A network Model Database of eukariotic transcription regulating sequences and proteins. Journal of Computational Biology, 1, 191-198.

Lefevre C. and Ikeda J. E. (1994). A fast word search algorithm for the representation of sequence similarity in genomic DNA. Nucleic Acids Res., 22, 404-411.

Levin J. M., Robson B. and Garnier J. (1986). An algorithm for secondary structure determination in proteins based on sequence similarity. FEBS Letters, 205, 303-308.

Levitt M. (1976). A simplified representation of protein conformations for rapid simulation of protein folding. J. Mol. Biol., 104, 59-107.

McNabb D. S., Xing Y. and Guarente L. (1995). Cloning of yeast HAP5: a novel subunit of a heterotrimeric complex required for CCAAT binding. Genes Dev., 9, 47-58.

Mengeritsky G. and Smith T. F. (1987). Recognition of characteristic patterns in sets of functionally equivalent DNA sequences. Comput. Appl. Biosci., 3, 223-227.

Needleman S. B. and Wunch C. D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48, 443-453.

Pearson W. R. and Lipman D. J. (1988). Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA, 85, 2444-2448.

Pearson W. R. (1990). Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol., 183, 63-98.

Pearson W. R. (1995). Comparison of methods for searching protein sequence databases. Protein Sci., 4, 1145-1160.

Perriere G., Gouy M. and Gojobori T. (1994). NRSub: a non-redundant data base for the Bacillus subtilis genome. Nucleic Acids Res., 22, 5525-5529.

Prunella N., Liuni S., Attimonelli M. and Pesole G. (1993). FASTPAT: a fast and efficient algorithm for string searching in DNA sequences. Comput. Appl. Biosci., 9, 541-545.

Risler J. L., Delorme M. O., Delacroix H. and Henaut A. (1988). Amino acid substitutions in structurally related proteins. A pattern recognition approach. J. Mol. Biol., 204, 1019-1029.

Roberts R. J. and Macelis D. (1994). REBASE-restriction enzymes and methylases. Nucleic Acids Res., 22, 3628-3639.

Schwartz R. M. and Dayhoff M. O. (1979). Matrices for detecting distant relationships. Atlas of Protein Structure, 5, Suppl. 3, 353-358.

Sibbald P. R. and Argos P. (1990). Scrutineer: a computer program that flexibly seeks and describes motifs and profiles in protein sequences databases. Comput. Appl. Biosci., 6, 279-288.

Smith T. F. and Waterman M. S. (1981). Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.

Sonnhammer E. L. and Kahn D. (1994). Modular arrangement of proteins as inferred from analysis of homology. Protein Sci., 3, 482-492.

Staden R. (1982). An interactive graphics program for comparing and aligning nucleic acid and amino acid sequences. Nucleic Acids Res., 10, 2951-2961.

Staden R. (1990). Searching for patterns in protein and nucleic acid sequences. Methods Enzymol., 183, 193-211.

States D.J. and Boguski M.S. (1991) Similarity and homology. In Sequence Analysis Primer, STOCKTON Press. 89-157.

Stormo G.D. (1990) Consensus patterns in DNA. Methods Enzymol., 183 211-221.

Sturrock S. S. and Collins J. F. (1994) MPsrch version 1.4. Edinburgh: University of Edinburgh Biocomputing Research Unit.

Taylor W.R. (1986). The clasification of amino acid conservation. J. Theor. Biol., 119 205- 218.

Trifonov E. N. and Brendel V. (1986). GNOMIC: A dictionary of genetic codes, Balabar Publishers. 272 pages.

Wallace J. C. and Henikoff S. (1992). PATMAT: a searching and extraction program for sequence, pattern and block queries and databases. Comput. Appl. Biosci., 8, 249-254.

Waterman M. S. (1989). Sequence alignments. In Mathematical methods for DNA Sequences. CRC Press.

Wingender E. (1994). Recognition of regulatory regions in genomic sequences. J. Biotech., 35, 273-280.

Vogt G., Etzold T. and Argos P. (1995). An assessment of amino acid exchange matrices in aligning protein sequences: the twilight zone revisited. J. Mol. Biol., 249, 816-831.

Wootton J. C. and Federhen S. (1993). Statistics of local complexity in amino acid sequences and sequence databases. Computers in Chemistry, 17, 149-163.

DSI Biologie moléculaire