{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,13]],"date-time":"2026-03-13T13:00:28Z","timestamp":1773406828206,"version":"3.50.1"},"reference-count":38,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2014,5,28]],"date-time":"2014-05-28T00:00:00Z","timestamp":1401235200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Bioinform Sys Biology"],"published-print":{"date-parts":[[2014,12]]},"DOI":"10.1186\/1687-4153-2014-8","type":"journal-article","created":{"date-parts":[[2014,5,28]],"date-time":"2014-05-28T01:02:43Z","timestamp":1401238963000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Application of discrete Fourier inter-coefficient difference for assessing genetic sequence similarity"],"prefix":"10.1186","volume":"2014","author":[{"given":"Brian R","family":"King","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maurice","family":"Aburdene","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alex","family":"Thompson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zach","family":"Warres","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2014,5,28]]},"reference":[{"key":"50_CR1","doi-asserted-by":"publisher","first-page":"356","DOI":"10.1017\/CBO9780511790492","volume-title":"Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids","author":"R Durbin","year":"1998","unstructured":"Durbin R, Eddy SR, Krogh A, Mitchison G: Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge, UK; 1998:356."},{"key":"50_CR2","doi-asserted-by":"publisher","first-page":"17077","DOI":"10.1073\/pnas.0909377106","volume":"106","author":"GE Sims","year":"2009","unstructured":"Sims GE, Jun S-R, Wu GA, Kim S-H: Whole-genome phylogeny of mammals: evolutionary information in genic and nongenic regions. Proc Natl Acad Sci U S A. 2009, 106: 17077-82. 10.1073\/pnas.0909377106","journal-title":"Proc Natl Acad Sci U S A"},{"key":"50_CR3","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1006\/mpev.2000.0785","volume":"16","author":"A Phillips","year":"2000","unstructured":"Phillips A, Janies D, Wheeler W: Multiple sequence alignment in phylogenetic analysis. Mol Phylogenet Evol. 2000, 16: 317-30. 10.1006\/mpev.2000.0785","journal-title":"Mol Phylogenet Evol"},{"key":"50_CR4","doi-asserted-by":"publisher","first-page":"356","DOI":"10.1017\/CBO9781139022095","volume-title":"Genomics and bioinformatics: an introduction to programming tools for life scientists","author":"T Samuelsson","year":"2012","unstructured":"Samuelsson T: Genomics and bioinformatics: an introduction to programming tools for life scientists. 1st edition. Cambridge University Press, Cambridge, UK; 2012:356.","edition":"1"},{"key":"50_CR5","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"S Altschul","year":"1990","unstructured":"Altschul S, Gish W, Miller W, Myers E, Lipman D: Basic local alignment search tool. J Mol Biol. 1990, 215: 403-410. 10.1016\/S0022-2836(05)80360-2","journal-title":"J Mol Biol"},{"key":"50_CR6","doi-asserted-by":"publisher","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","volume":"22","author":"JD Thompson","year":"1994","unstructured":"Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22: 4673-4680. 10.1093\/nar\/22.22.4673","journal-title":"Nucleic Acids Res"},{"key":"50_CR7","doi-asserted-by":"publisher","first-page":"419","DOI":"10.1093\/bib\/bbt078","volume":"15","author":"L Pinello","year":"2013","unstructured":"Pinello L, Lo Bosco G, Yuan G-C: Applications of alignment-free methods in epigenomics. Brief Bioinform. 2013, 15: 419-430.","journal-title":"Brief Bioinform"},{"key":"50_CR8","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1093\/bioinformatics\/btg005","volume":"19","author":"S Vinga","year":"2003","unstructured":"Vinga S, Almeida J: Alignment-free sequence comparison\u2013a review. Bioinformatics. 2003, 19: 513-523. 10.1093\/bioinformatics\/btg005","journal-title":"Bioinformatics"},{"key":"50_CR9","series-title":"Brief Bioinform","volume-title":"Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis","author":"O Bonham-Carter","year":"2013","unstructured":"Bonham-Carter O, Steele J, Bastola D: Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis. Brief Bioinform. online only, published July 31, 2013"},{"key":"50_CR10","doi-asserted-by":"publisher","first-page":"1466","DOI":"10.1093\/bioinformatics\/btr176","volume":"27","author":"M Domazet-Lo\u0161o","year":"2011","unstructured":"Domazet-Lo\u0161o M, Haubold B: Alignment-free detection of local similarity among viral and bacterial genomes. Bioinformatics. 2011, 27: 1466-72. 10.1093\/bioinformatics\/btr176","journal-title":"Bioinformatics"},{"key":"50_CR11","first-page":"249","volume-title":"Proceedings of 5th International Conference of Foundations of Data Organization \u2013 FODO '98","author":"D Rafiei","year":"1998","unstructured":"Rafiei D, Mendelzon A: Efficient Retrieval of Similar Time Sequences Using DFT. In Proceedings of 5th International Conference of Foundations of Data Organization \u2013 FODO '98. Kobe, Japan; 1998:249-257."},{"key":"50_CR12","doi-asserted-by":"publisher","first-page":"488","DOI":"10.1145\/354756.354857","volume-title":"Proc. ninth Int. Conf. Inf. Knowl. Manag. - CIKM \u201900","author":"Y-L Wu","year":"2000","unstructured":"Wu Y-L, Agrawal D, El Abbadi A: A comparison of DFT and DWT based similarity search in time-series databases. In Proc. ninth Int. Conf. Inf. Knowl. Manag. - CIKM \u201900. ACM Press, New York, USA; 2000:488-495."},{"key":"50_CR13","doi-asserted-by":"publisher","first-page":"279","DOI":"10.1111\/j.1582-4934.2002.tb00196.x","volume":"6","author":"PD Cristea","year":"2002","unstructured":"Cristea PD: Conversion of nucleotides sequences into genomic signals. J Cell Mol Med. 2002, 6: 279-303. 10.1111\/j.1582-4934.2002.tb00196.x","journal-title":"J Cell Mol Med"},{"key":"50_CR14","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1109\/79.939833","volume":"18","author":"D Anastassiou","year":"2001","unstructured":"Anastassiou D: Genomic signal processing. IEEE Signal Process Mag. 2001, 18: 8-20.","journal-title":"IEEE Signal Process Mag"},{"key":"50_CR15","first-page":"71","volume":"2011","author":"SD Sharma","year":"2011","unstructured":"Sharma SD, Shakya K, Sharma SN: Evaluation of DNA mapping schemes for exon detection. Int Conf Comput Commun Electr Technol. 2011, 2011: 71-74.","journal-title":"Int Conf Comput Commun Electr Technol"},{"key":"50_CR16","doi-asserted-by":"publisher","first-page":"3059","DOI":"10.1093\/nar\/gkf436","volume":"30","author":"K Katoh","year":"2002","unstructured":"Katoh K, Misawa K, Kuma K, Miyata T: MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002, 30: 3059-3066. 10.1093\/nar\/gkf436","journal-title":"Nucleic Acids Res"},{"key":"50_CR17","doi-asserted-by":"publisher","first-page":"3805","DOI":"10.1103\/PhysRevLett.68.3805","volume":"68","author":"RF Voss","year":"1992","unstructured":"Voss RF: Evolution of long-range fractal correlations and 1\/f noise in DNA base sequences. Phys Rev Lett. 1992, 68: 3805-3808. 10.1103\/PhysRevLett.68.3805","journal-title":"Phys Rev Lett"},{"key":"50_CR18","doi-asserted-by":"publisher","first-page":"3064","DOI":"10.1093\/bioinformatics\/btp546","volume":"25","author":"V Afreixo","year":"2009","unstructured":"Afreixo V, Bastos CAC, Pinho AJ, Garcia SP, Ferreira PJSG: Genome analysis with inter-nucleotide distances. Bioinformatics. 2009, 25: 3064-70. 10.1093\/bioinformatics\/btp546","journal-title":"Bioinformatics"},{"key":"50_CR19","first-page":"1","volume":"3","author":"MK Hota","year":"2010","unstructured":"Hota MK, Srivastava VK: Performance analysis of different DNA to numerical mapping techniques for identification of protein coding regions using tapered window based short-time discrete Fourier transform. Int Conf Power, Control Embed Syst. 2010, 3: 1-4.","journal-title":"Int Conf Power, Control Embed Syst"},{"key":"50_CR20","doi-asserted-by":"publisher","first-page":"310","DOI":"10.1109\/JSTSP.2008.923854","volume":"2","author":"M Akhtar","year":"2008","unstructured":"Akhtar M, Epps J, Ambikairajah E: Signal processing in sequence analysis: advances in eukaryotic gene prediction. IEEE J Sel Top Signal Process. 2008, 2: 310-321.","journal-title":"IEEE J Sel Top Signal Process"},{"key":"50_CR21","first-page":"355","volume-title":"Proc. 2012 IEEE Symp. Ind. Electron. Appl. (ISIEA2012)","author":"H Saberkari","year":"2012","unstructured":"Saberkari H, Shamsi M, Sedaaghi M, Golabi F: Prediction of protein coding regions in DNA sequences using signal processing methods. In Proc. 2012 IEEE Symp. Ind. Electron. Appl. (ISIEA2012). Bandung, Indonesia; 2012:355-360."},{"key":"50_CR22","doi-asserted-by":"publisher","first-page":"370","DOI":"10.1109\/TCSI.2007.910541","volume":"55","author":"KD Rao","year":"2008","unstructured":"Rao KD, Member S, Swamy MNS, Fellow L: Analysis of genomics and proteomics using DSP techniques. IEEE Trans Circuits Syst I Regul Pap. 2008, 55: 370-378.","journal-title":"IEEE Trans Circuits Syst I Regul Pap"},{"key":"50_CR23","doi-asserted-by":"publisher","first-page":"639","DOI":"10.1089\/cmb.2010.0184","volume":"18","author":"SA Marhon","year":"2011","unstructured":"Marhon SA, Kremer SC: Gene prediction based on DNA spectral analysis: a literature review. J Comput Biol. 2011, 18: 639-76. 10.1089\/cmb.2010.0184","journal-title":"J Comput Biol"},{"key":"50_CR24","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1109\/MSPEC.1967.5217220","volume":"4","author":"EO Brigham","year":"1967","unstructured":"Brigham EO, Morrow RE: The fast Fourier transform. IEEE Spectr. 1967, 4: 63-70.","journal-title":"IEEE Spectr"},{"key":"50_CR25","volume-title":"Understanding Digital Signal Processing","author":"RG Lyons","year":"2004","unstructured":"Lyons RG: Understanding Digital Signal Processing. Pearson Education, Upper Saddle River, NJ; 2004."},{"key":"50_CR26","volume-title":"Discrete-Time Signal Processing","author":"AV Oppenheim","year":"2010","unstructured":"Oppenheim AV, Schafer RW: Discrete-Time Signal Processing. 3rd edition. Prentice Hall, Upper Saddle River, NJ, USA; 2010.","edition":"3"},{"key":"50_CR27","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1016\/j.jfranklin.2003.12.001","volume":"341","author":"P Vaidyanathan","year":"2004","unstructured":"Vaidyanathan P: The role of signal-processing concepts in genomics and proteomics. J Franklin Inst. 2004, 341: 111-135. 10.1016\/j.jfranklin.2003.12.001","journal-title":"J Franklin Inst"},{"key":"50_CR28","volume-title":"IEEE Work. Genomic Signal Process. Stat. (GENSIPS)","author":"JA Berger","year":"2002","unstructured":"Berger JA, Mitra SK, Carli M, Neri A: New approaches to genome sequence analysis based on digital signal processing. In IEEE Work. Genomic Signal Process. Stat. (GENSIPS). IEEE Press, Raleigh, North Carolina, USA; 2002."},{"key":"50_CR29","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1109\/JSTSP.2008.923851","volume":"2","author":"J Tuqan","year":"2008","unstructured":"Tuqan J, Rushdi A, Member S: A DSP approach for finding the codon bias in DNA sequences. IEEE J Sel Top Signal Process. 2008, 2: 343-356.","journal-title":"IEEE J Sel Top Signal Process"},{"key":"50_CR30","doi-asserted-by":"publisher","first-page":"1073","DOI":"10.1093\/bioinformatics\/16.12.1073","volume":"16","author":"D Anastassiou","year":"2000","unstructured":"Anastassiou D: Frequency-domain analysis of biomolecular sequences. Bioinformatics. 2000, 16: 1073-1081. 10.1093\/bioinformatics\/16.12.1073","journal-title":"Bioinformatics"},{"key":"50_CR31","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1109\/NEBC.1989.36756","volume-title":"Proc. Fifteenth Annu. Northeast Bioeng. Conf","author":"EA Cheever","year":"1989","unstructured":"Cheever EA, Searls DB, Karunaratne W, Overton GC: Using Signal Processing Techniques for DNA Sequence Comparison. In Proc. Fifteenth Annu. Northeast Bioeng. Conf. IEEE Press, Boston, MA; 1989:173-174."},{"key":"50_CR32","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1016\/0022-2836(70)90057-4","volume":"48","author":"SB Needleman","year":"1970","unstructured":"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: 443-453. 10.1016\/0022-2836(70)90057-4","journal-title":"J Mol Biol"},{"key":"50_CR33","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1016\/0025-5564(81)90043-2","volume":"53","author":"DF Robinson","year":"1981","unstructured":"Robinson DF, Foulds LR: Comparison of phylogenetic trees. Math Biosci. 1981, 53: 131-147. 10.1016\/0025-5564(81)90043-2","journal-title":"Math Biosci"},{"key":"50_CR34","doi-asserted-by":"publisher","first-page":"592","DOI":"10.1093\/bioinformatics\/btq706","volume":"27","author":"KP Schliep","year":"2011","unstructured":"Schliep KP: phangorn: phylogenetic analysis in R. Bioinformatics. 2011, 27: 592-3. 10.1093\/bioinformatics\/btq706","journal-title":"Bioinformatics"},{"key":"50_CR35","doi-asserted-by":"publisher","first-page":"7639","DOI":"10.1073\/pnas.78.12.7639","volume":"78","author":"GM Air","year":"1981","unstructured":"Air GM: Sequence relationships among the hemagglutinin genes of 12 subtypes of influenza A virus. Proc Natl Acad Sci U S A. 1981, 78: 7639-43. 10.1073\/pnas.78.12.7639","journal-title":"Proc Natl Acad Sci U S A"},{"key":"50_CR36","doi-asserted-by":"publisher","first-page":"2947","DOI":"10.1093\/bioinformatics\/btm404","volume":"23","author":"MA Larkin","year":"2007","unstructured":"Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG: Clustal W and Clustal X version 2.0. Bioinformatics. 2007, 23: 2947-8. 10.1093\/bioinformatics\/btm404","journal-title":"Bioinformatics"},{"key":"50_CR37","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1038\/msb.2011.75","volume":"7","author":"F Sievers","year":"2011","unstructured":"Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, S\u00f6ding J, Thompson JD, Higgins DG: Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011, 7: 539.","journal-title":"Mol Syst Biol"},{"key":"50_CR38","doi-asserted-by":"crossref","first-page":"709","DOI":"10.1093\/oso\/9780195079517.001.0001","volume-title":"The origins of order, vol. 209","author":"S Kaufmann","year":"1993","unstructured":"Kaufmann S: The origins of order, vol. 209. Oxford University Press, Oxford, UK; 1993:709."}],"container-title":["EURASIP Journal on Bioinformatics and Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1687-4153-2014-8\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1687-4153-2014-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1687-4153-2014-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,27]],"date-time":"2024-05-27T02:54:16Z","timestamp":1716778456000},"score":1,"resource":{"primary":{"URL":"https:\/\/bsb-eurasipjournals.springeropen.com\/articles\/10.1186\/1687-4153-2014-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,5,28]]},"references-count":38,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2014,12]]}},"alternative-id":["50"],"URL":"https:\/\/doi.org\/10.1186\/1687-4153-2014-8","relation":{},"ISSN":["1687-4153"],"issn-type":[{"value":"1687-4153","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,5,28]]},"assertion":[{"value":"16 December 2013","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 May 2014","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"28 May 2014","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"8"}}