Bibliography

Attwood T. K., Croning M. D. R., Flower D. R., Lewis A. P., Mabey J. E., Scordis P., Selley J. N. and Wright W. 2000. PRINTS-S: the database formerly known as PRINTS. Nucleic Acids Research, 28, 225-227.

Bailey T. L., Williams N., Misleh C. and Li W. W. 2006. MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Research, 34, W369-W373.

Barker W. C., Garavelli J. S., Huang H., McGarvey P. B., Orcutt B. C., Srinivasarao G. Y., Xiao C, Yeh L. L., Ledley R . S., Janda J. F., Pfeiffer F., Mewes H. W., Tsugita A. and Wu C. 2000. The Protein Information Resource (PIR). Nucleic Acids Research, 28, 41-44.

Benson D. A., Karsch-Mizrachi I., Lipman D. J. and Ostell J. 2006. GenBank. Nucleic Acids Research, 34, D16–D20.

Berman H. M., Westbrook J., Feng Z., Gilliland G., Bhat T. N., Weissig H., Shindyalov I. N. and Bourne P. E. 2000. The Protein DataBank. Nucleic Acids Research, 28, 235-242.

Blake J. A., Bult C. J., Eppig J. T., Kadin J. A. and Richardson J. E. 2007. The mouse genome database (MGDB): new features facilitating a model system. Nucleic Acids Research, 35, D630-D637.

Blake J. A., Eppig J. T., Bult C. J., Kadin J. A. and Richardson J. E. 2006. The Mouse Genome Database (MGD): updates and enhancements. Nucleic Acids Research, 34, D562–D567.

Brent M. R., Guigo R. 2004. Recent advances in gene structure prediction. Current Opinion in Structural Biology, 14, 264–272 .

Boeckmann B., Bairoch A., Apweiler R., Blatter M. C., Estreicher A., Gasteiger E., Martin M. J., Michoud K., Donovan C. O., Phan I., Pilbout S. and Schneider M. 2003. The SWISS-PROT protein knowledgebase and its supplement TrEMBL. Nucleic Acids Research, 31, 365-370.

Brazma A., Hingamp P., Quackenbush J., Sherlock G., Spellman P., Stoeckert C., Aach J., Ansorge W., Ball C. A. and Causton H. C. 2001. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nature Genetics, 29, 365-371.

Brooksbank C., Camon E., Harris M. A., Magrane M., Martin M. J., Mulder N., O’Donovan C., Parkinson H. and Tuli M. A. 2003. The European Bioinformatics Institute’s data resources. Nucleic Acids Research, 31, 43–50.

Christian J. A. S., Cerutti L., Hulo N., Gattiker., Falquet L., Pagni M., Bairoch A.  and Bucher P. 2002. PROSITE: A documented database using patterns and profiles as motif descriptors. Briefings in Bioinformatics, 3, 265-274.

Clowney L., Jain S.C., Srinivasan A. R., Westbrook J., Olson W. K. and Berman H. M. 1996. Geometric Parameters in Nucleic Acids: Nitrogenous Bases. Journal of the American Chemical Society, 118, 509– 518.

Corpet F., Gouzy J., Kahn D. 1998. The ProDom database of protein domain families. Nucleic Acids Research, 26, 323-326.

Gasteiger E., Jung E. and Bairoch A. 2001. SWISS-PROT: connecting biomolecular knowledge via a protein database. Current Issues in Molecular Biology, 3, 47–55.

Finn R. D., Mistry J., Schuster-Böckler B., Griffiths-Jones S., Hollich V., Lassmann T., Moxon S., Marshall M., Khanna A., Durbin R., Eddy S. R., Sonnhammer E. L. L. and Bateman A. 2006. Pfam: clans, web tools and services. Nucleic Acids Research, 34, D247-D251.

Florence Corpet, Florence Servant, Jérôme Gouzy and Daniel Kahn. 2000. ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons.  Nucleic Acids Research, 28, 267-269.

Gelbin A., Schneider B., Clowney L., Hsieh S. H., Olson W. K. and Berman H. M. 1996. Geometric Parameters in Nucleic Acids: Sugar and Phosphate Constituents. Journal of the American Chemical Society, 118, 519–528.

Hang Chen H., Gu F and Huang Z. 2006. Improved Chou-Fasman method for protein secondary structure prediction. BMC Bioinformatics, 7, S14.

Harte N., Silventoinen V., Ouevillon E., Robinson S., Kallio K., Fustero X., Patel P., Jokinen P. and Lopez R. 2004. Public web-based services from the European Bioinformatics Institute. Nucleic Acids Research, 32, W3-W9.

Kans J.and Ouellette B. 2001. In: Baxevanis E.D., Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins. John Wiley and Sons, Pp. 65–81.

Kapushesky M., Kemmeren P., Culhane A. C., Durinck S., Ihmels J., Korner C., Kull M., Torrente A., Sarkans U. and Vilo J. 2004. Expression Profiler: next generation—an online platform for analysis of microarray data. Nucleic Acids Research, 32, W465–W470.

Karsch-Mizrachi I., Benson D. A., Lipman D. J., Ostell J. and Wheeler D. L. 2007. GenBanK. Nucleic Acids Research, 35, D21-D25.

Leinonen R., Nardone F., Oyewole O., Redaschi N. and Stoehr P. 2003. The EMBL SVA. Bioinformatics, 19, 1861–1862.

Ogata H., Goto S., Sato K, Fujibuchi W., Bono H. and Kanehis M. 1999. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Research, 27, 29-34.

Parkinson H., Kapushesky M., Sarkans U., Shojatalab M., Abeygunawardena N., Coulson R., Farne A., Holloway E., Kolesnykov N., Lilja P., Lukk M., Mani R., Rayner T., Sharma A., William E. and Brazma A. 2007. ArrayExpress—a public database of microarray experiments and gene expression profiles. Nucleic Acids Research, 35, D747-D750.

Parkinson H. and Sarkans U. 2005. ArrayExpress— a public repository for microarray gene expression data at the EBI. Nucleic Acids Research, 33, D553 – D555.

Prevelige P., Fasman G. D. 1989. Chou-Fasman prediction of the secondary structure of proteins. The Chou-Fasman –Previlge Algorithm, 9, 391-395.

Stoesser G., Baker W., Vanden B. A., Camon E., Garcia-Pastor M., Kanz C., Kulikova T., Leinonen R., Lin O. and Lombard V. 2002. The EMBL Nucleotide Sequence Database. Nucleic Acids Research, 30, 21-26.

Stupka E. 2002. Current Opinion in Molecular Theory, 4, 265-74. Tamara K., Ruth A., Aldebert P., Althorpe N., Andersson M., Baldwin A., Bates K., Bhattacharyya S., Bower L., Browne P., Castro M., Cochrane G., Duggan K., Eberhardt R., Faruque N., Hoad G., Kanz C., Lee C., Leinonen R., Lin Q., Lombard V., Lopez R., Lorenc D., McWilliam H., Mukherjee G., Nardone F., Pastor M. P. G., Plaister S., Sobhany S., Stoehr P., Vaughan R., Wu D., Zhu W. and Apweiler R. 2007. EMBL Nucleotide Sequence Database in 2006. Nucleic Acids Research, 35, D16-D20.