{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,14]],"date-time":"2026-03-14T21:39:46Z","timestamp":1773524386337,"version":"3.50.1"},"publisher-location":"Berlin, Heidelberg","reference-count":31,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"value":"9783540200765","type":"print"},{"value":"9783540397632","type":"electronic"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2003]]},"DOI":"10.1007\/978-3-540-39763-2_32","type":"book-chapter","created":{"date-parts":[[2010,6,25]],"date-time":"2010-06-25T20:49:30Z","timestamp":1277498970000},"page":"447-461","source":"Crossref","is-referenced-by-count":13,"title":["Composition Alignment"],"prefix":"10.1007","author":[{"given":"Gary","family":"Benson","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"key":"32_CR1","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1006\/jagm.2000.1120","volume":"37","author":"A. Amir","year":"2000","unstructured":"Amir, A., Aumann, Y., Landau, G., Lewenstein, M., Lewenstein, N.: Pattern matching with swaps. J. Algorithms\u00a037, 247\u2013266 (2000)","journal-title":"J. Algorithms"},{"key":"32_CR2","unstructured":"Amir, A., Cole, R., Hariharan, R., Lewenstein, M., Porat, E.: Overlap matching. In: Proc. 12th ACM-SIAM Sym. on Discrete Algorithms, pp. 279\u2013288 (2001)"},{"key":"32_CR3","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1016\/S0020-0190(01)00302-7","volume":"83","author":"A. Amir","year":"2002","unstructured":"Amir, A., Lewenstein, M., Porat, E.: Approximate swapped matching. Information Processing Letters\u00a083, 33\u201339 (2002)","journal-title":"Information Processing Letters"},{"key":"32_CR4","doi-asserted-by":"publisher","first-page":"200","DOI":"10.1214\/aoap\/1177005208","volume":"4","author":"R. Arratia","year":"1994","unstructured":"Arratia, R., Waterman, M.: A phase transition for the score in matching random sequences allowing deletions. Ann. Appl. Prob.\u00a04, 200\u2013225 (1994)","journal-title":"Ann. Appl. Prob."},{"key":"32_CR5","doi-asserted-by":"publisher","first-page":"425","DOI":"10.1006\/jmbi.1996.0035","volume":"255","author":"C.J. Benham","year":"1996","unstructured":"Benham, C.J.: Duplex destabilization in superhelical DNA is predicted to occur at specific transcriptional regulatory regions. J. Mol. Biol.\u00a0255, 425\u2013434 (1996)","journal-title":"J. Mol. Biol."},{"key":"32_CR6","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1090\/dimacs\/047\/08","volume":"47","author":"C.J. Benham","year":"1999","unstructured":"Benham, C.J.: The topologically driven strand separation transition in DNAmethods of analysis and biological significance. DIMACS Series in Discrete Mathematics and Theoretical Computer Science\u00a047, 173\u2013198 (1999)","journal-title":"DIMACS Series in Discrete Mathematics and Theoretical Computer Science"},{"key":"32_CR7","doi-asserted-by":"publisher","first-page":"637","DOI":"10.1146\/annurev.ge.23.120189.003225","volume":"23","author":"G. Bernardi","year":"1989","unstructured":"Bernardi, G.: The isochore organization of the human genome. Annu. Rev. Genet.\u00a023, 637\u2013661 (1989)","journal-title":"Annu. Rev. Genet."},{"key":"32_CR8","doi-asserted-by":"publisher","first-page":"445","DOI":"10.1146\/annurev.ge.29.120195.002305","volume":"29","author":"G. Bernardi","year":"1995","unstructured":"Bernardi, G.: The human genome: Organization and evolutionary history. Annu. Rev. Genet.\u00a029, 445\u2013476 (1995)","journal-title":"Annu. Rev. Genet."},{"key":"32_CR9","doi-asserted-by":"publisher","first-page":"563","DOI":"10.1016\/0022-2836(90)90223-9","volume":"212","author":"P. Bucher","year":"1990","unstructured":"Bucher, P.: Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J. Mol. Biol.\u00a0212, 563\u2013578 (1990)","journal-title":"J. Mol. Biol."},{"key":"32_CR10","volume-title":"Introduction to Algorithms","author":"T. Cormen","year":"1990","unstructured":"Cormen, T., Leiserson, C., Rivest, R.: Introduction to Algorithms. MIT Press, Cambridge (1990)"},{"key":"32_CR11","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1146\/annurev.bi.52.070183.000521","volume":"52","author":"W. Doerfler","year":"1983","unstructured":"Doerfler, W.: DNA methylation and gene activity. Ann. Rev. Biochem.\u00a052, 93\u2013124 (1983)","journal-title":"Ann. Rev. Biochem."},{"key":"32_CR12","doi-asserted-by":"crossref","unstructured":"Felsenfeld, G., McGhee, J.: Methylation and gene activity (1982)","DOI":"10.1038\/296602a0"},{"key":"32_CR13","doi-asserted-by":"publisher","first-page":"261","DOI":"10.1016\/0022-2836(87)90689-9","volume":"196","author":"M.G. Garden","year":"1987","unstructured":"Garden, M.G., Frommer, M.: CpG islands in vertebrate genomes. J.Mol. Biol.\u00a0196, 261\u2013282 (1987)","journal-title":"J.Mol. Biol."},{"key":"32_CR14","doi-asserted-by":"publisher","first-page":"5497","DOI":"10.1093\/nar\/22.24.5497","volume":"22","author":"D.S. Goodsell","year":"1994","unstructured":"Goodsell, D.S., Dickerson, R.E.: Bending and curvature calculations in B-DNA. Nucleic Acids Research\u00a022, 5497\u20135503 (1994)","journal-title":"Nucleic Acids Research"},{"key":"32_CR15","doi-asserted-by":"publisher","first-page":"705","DOI":"10.1016\/0022-2836(82)90398-9","volume":"162","author":"O. Gotoh","year":"1982","unstructured":"Gotoh, O.: An improved algorithm for matching biological sequences. J. Mol. Biol.\u00a0162, 705\u2013708 (1982)","journal-title":"J. Mol. Biol."},{"key":"32_CR16","doi-asserted-by":"publisher","first-page":"318","DOI":"10.1093\/nar\/27.1.318","volume":"27","author":"T. Heinemeyer","year":"1999","unstructured":"Heinemeyer, T., Chen, X., Karas, H., Kel, A., Kel, O., Liebich, I., Meinhardt, T., Reuter, I., Schacherer, F., Wingender, E.: Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms. Nucleic Acids Res.\u00a027, 318\u2013322 (1999)","journal-title":"Nucleic Acids Res."},{"key":"32_CR17","doi-asserted-by":"publisher","first-page":"2264","DOI":"10.1073\/pnas.87.6.2264","volume":"87","author":"S. Karlin","year":"1990","unstructured":"Karlin, S., Altschul, S.: Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl. Acad. Sci. USA\u00a087, 2264\u20132268 (1990)","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"32_CR18","doi-asserted-by":"publisher","first-page":"501","DOI":"10.1038\/320501a0","volume":"320","author":"H.-S. Koo","year":"1986","unstructured":"Koo, H.-S., Wu, H.-M., Crothers, D.M.: DNA bending at adenine - thymine tracts. Nature\u00a0320, 501\u2013506 (1986)","journal-title":"Nature"},{"key":"32_CR19","doi-asserted-by":"publisher","first-page":"1247","DOI":"10.1126\/science.271.5253.1247","volume":"271","author":"M. Lewis","year":"1996","unstructured":"Lewis, M., Chang, G., Horton, N.C., Kercher, M.A., Pace, H.C., Schumacher, M.A., Brennan, R.G., Lu, P.: Crystal structure of the lactose operon repressor and its complexes with DNA and inducer. Science\u00a0271, 1247\u20131254 (1996)","journal-title":"Science"},{"key":"32_CR20","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1109\/18.61115","volume":"37","author":"J. Lin","year":"1991","unstructured":"Lin, J.: Divergence measures based on the Shannon entropy. IEEE Trans. Inf. Theor.\u00a037, 145\u2013151 (1991)","journal-title":"IEEE Trans. Inf. Theor."},{"key":"32_CR21","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1145\/321879.321880","volume":"22","author":"R. Lowrance","year":"1975","unstructured":"Lowrance, R., Wagner, R.A.: An extension of the string-to-string correction problem. JACM\u00a022, 177\u2013183 (1975)","journal-title":"JACM"},{"key":"32_CR22","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1016\/0022-2836(70)90057-4","volume":"48","author":"S. Needleman","year":"1970","unstructured":"Needleman, S., Wunch, C.: A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol.\u00a048, 443\u2013453 (1970)","journal-title":"J. Mol. Biol."},{"key":"32_CR23","doi-asserted-by":"publisher","first-page":"302","DOI":"10.1093\/nar\/28.1.302","volume":"28","author":"R. P\u00e9rier","year":"2000","unstructured":"P\u00e9rier, R., Praz, V., Junier, T., Bonnard, C., Bucher, P.: The Eukaryotic Promoter Database (EPD). Nucleic Acids Research\u00a028, 302\u2013303 (2000)","journal-title":"Nucleic Acids Research"},{"key":"32_CR24","doi-asserted-by":"publisher","first-page":"1001","DOI":"10.1126\/science.1653449","volume":"253","author":"S.C. Schultz","year":"1991","unstructured":"Schultz, S.C., Shields, G.C., Steitz, T.A.: Crystal structure of a CAP-DNA complex: The DNA is bent by 90 degrees. Science\u00a0253, 1001\u20131007 (1991)","journal-title":"Science"},{"key":"32_CR25","doi-asserted-by":"publisher","first-page":"743","DOI":"10.1016\/S0959-437X(96)80030-X","volume":"6","author":"A. Smit","year":"1996","unstructured":"Smit, A.: The origin of interspersed repeats in the human genome. Curr. Opin. Genet. Dev.\u00a06, 743\u2013748 (1996)","journal-title":"Curr. Opin. Genet. Dev."},{"key":"32_CR26","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1016\/0022-2836(81)90087-5","volume":"147","author":"T. Smith","year":"1981","unstructured":"Smith, T., Waterman, M.: Identification of common molecular subsequences. J. Mol. Biol.\u00a0147, 195\u2013197 (1981)","journal-title":"J. Mol. Biol."},{"key":"32_CR27","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/S0022-2836(05)80006-3","volume":"235","author":"M. Vingron","year":"1994","unstructured":"Vingron, M., Waterman, M.: Sequence alignment and penalty choice: review of concepts, case studies and implications. J. Mol. Biol.\u00a0235, 1\u201312 (1994)","journal-title":"J. Mol. Biol."},{"key":"32_CR28","doi-asserted-by":"crossref","unstructured":"Wagner, R.A.: On the complexity of the extended string-to-string correction problem. In: Proceedings 7th ACM STOC, pp. 218\u2013223 (1975)","DOI":"10.1145\/800116.803771"},{"key":"32_CR29","doi-asserted-by":"publisher","first-page":"1239","DOI":"10.1073\/pnas.84.5.1239","volume":"84","author":"M. Waterman","year":"1987","unstructured":"Waterman, M., Gordon, L., Arratia, R.: Phase transitions in sequence matches and nucleic acid structure. Proc. Natl. Acad. Sci. USA\u00a084, 1239\u20131243 (1987)","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"32_CR30","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1016\/S0378-1119(00)00301-2","volume":"255","author":"E. Yeramian","year":"2000","unstructured":"Yeramian, E.: Genes and the physics of the DNA double-helix. Gene\u00a0255, 139\u2013150 (2000)","journal-title":"Gene"},{"key":"32_CR31","doi-asserted-by":"publisher","first-page":"190","DOI":"10.1093\/bioinformatics\/18.1.190","volume":"18","author":"E. Yeraminan","year":"2002","unstructured":"Yeraminan, E., Bonnefoy, S., Langsley, G.: Physics-based gene identification: proof of concept for Plasmodium falciparum. Bioinformatics\u00a018, 190\u2013193 (2002)","journal-title":"Bioinformatics"}],"container-title":["Lecture Notes in Computer Science","Algorithms in Bioinformatics"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-540-39763-2_32","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,30]],"date-time":"2019-05-30T12:52:32Z","timestamp":1559220752000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-540-39763-2_32"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2003]]},"ISBN":["9783540200765","9783540397632"],"references-count":31,"URL":"https:\/\/doi.org\/10.1007\/978-3-540-39763-2_32","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"value":"0302-9743","type":"print"},{"value":"1611-3349","type":"electronic"}],"subject":[],"published":{"date-parts":[[2003]]}}}