{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T10:35:12Z","timestamp":1761561312054},"reference-count":32,"publisher":"Springer Science and Business Media LLC","issue":"S1","license":[{"start":{"date-parts":[[2009,1,1]],"date-time":"2009-01-01T00:00:00Z","timestamp":1230768000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2009,1]]},"DOI":"10.1186\/1471-2105-10-s1-s17","type":"journal-article","created":{"date-parts":[[2009,1,30]],"date-time":"2009-01-30T15:04:49Z","timestamp":1233327889000},"source":"Crossref","is-referenced-by-count":9,"title":["Short read DNA fragment anchoring algorithm"],"prefix":"10.1186","volume":"10","author":[{"given":"Wendi","family":"Wang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peiheng","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xinchun","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2009,1,30]]},"reference":[{"key":"3200_CR1","unstructured":"Genome Analyzer System[ http:\/\/www.illumina.com\/ ]"},{"key":"3200_CR2","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1101\/gr.7.5.401","volume":"7","author":"James L Weber","year":"1997","unstructured":"Weber JamesL, Myers EugeneW: Human Whole-Genome Shotgun Sequencing. Genome Res 1997, 7: 401\u2013409.","journal-title":"Genome Res"},{"key":"3200_CR3","doi-asserted-by":"publisher","first-page":"1725","DOI":"10.1101\/gr.194201","volume":"11","author":"Z Ning","year":"2001","unstructured":"Ning Z, Cox AJ, Mullikin JC: SSAHA: A fast search method for large DNA databases. Genome Res 2001, 11: 1725\u20131729.","journal-title":"Genome Res"},{"key":"3200_CR4","doi-asserted-by":"crossref","unstructured":"Chaisson MJ, Pevzner PA: Short read fragment assembly of bacterial genomes. Genome Res 18(2):324\u2013330. February 1, 2008 February 1, 2008","DOI":"10.1101\/gr.7088808"},{"key":"3200_CR5","doi-asserted-by":"publisher","first-page":"713","DOI":"10.1093\/bioinformatics\/btn025","volume":"24","author":"Li Ruiqiang","year":"2008","unstructured":"Ruiqiang Li, et al.: SOAP: short oligonucleotide alignment program. Bioinformatics 2008, 24: 713\u2013714.","journal-title":"Bioinformatics"},{"key":"3200_CR6","unstructured":"Francisco M, Marth GaborT, Granger S: Computational tools for next-generation sequencing applications. Pacific Symposium on Biocomputing 13: 87\u201389."},{"issue":"1","key":"3200_CR7","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1016\/0022-2836(81)90087-5","volume":"147","author":"TF Smith","year":"1981","unstructured":"Smith TF, Waterman MS: Identification of Common Molecular Subsequences. Journal of Molecular Biology 1981, 147(1):195\u2013197.","journal-title":"Journal of Molecular Biology"},{"issue":"1","key":"3200_CR8","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1145\/375360.375365","volume":"33","author":"G Navarro","year":"2001","unstructured":"Navarro G: A guided tour to approximate string matching. ACM Computing Surveys 2001, 33(1):31\u201388.","journal-title":"ACM Computing Surveys"},{"key":"3200_CR9","doi-asserted-by":"publisher","first-page":"2444","DOI":"10.1073\/pnas.85.8.2444","volume":"85","author":"WR Pearson","year":"1988","unstructured":"Pearson WR, Lipman DJ: Improved tools for biological sequence comparison. Proc Natl Acad Sci 1988, 85: 2444\u20132448.","journal-title":"Proc Natl Acad Sci"},{"key":"3200_CR10","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215: 403\u2013410.","journal-title":"J Mol Biol"},{"key":"3200_CR11","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1111\/j.1432-1033.1970.tb01046.x","volume":"16","author":"AJ Gibbs","year":"1970","unstructured":"Gibbs AJ, McIntyre GA: The diagram, a method for comparing sequences. It's use with amino acid and nucleotide sequences. Eur J Biochem 1970, 16: 1\u201311.","journal-title":"Eur J Biochem"},{"key":"3200_CR12","volume-title":"Fourth IEEE symposium on bioinformatics and bioengineering (BIBE'04), Taichung, Taiwan","author":"G Cooper","year":"2004","unstructured":"Cooper G, Raymer M, Doom T, Krane D, Futamur N: Indexing genomic databases. Fourth IEEE symposium on bioinformatics and bioengineering (BIBE'04), Taichung, Taiwan 2004."},{"key":"3200_CR13","first-page":"351","volume-title":"VLDB, Roma, Italy","author":"T Kahveci","year":"2001","unstructured":"Kahveci T, Singh AK: An Efficient Index Structure for String Databases. VLDB, Roma, Italy 2001, 351\u2013360."},{"key":"3200_CR14","first-page":"251","volume-title":"Algorithmica","author":"E Myers","year":"1986","unstructured":"Myers E: An O(ND) difference algorithm and its variations. Algorithmica 1986, 251\u2013266."},{"key":"3200_CR15","first-page":"202","volume-title":"Proceedings of the 9th ACM International Conference on Information and Knowledge Management (CIKM), Washington, DC, USA","author":"H Ferhatosmanoglu","year":"2000","unstructured":"Ferhatosmanoglu H, Tuncel E, Agrawal D, El Abbadi A: Vector Approximation based Indexing for Non-uniform High Dimensional Data Sets. Proceedings of the 9th ACM International Conference on Information and Knowledge Management (CIKM), Washington, DC, USA 2000, 202\u2013209."},{"key":"3200_CR16","first-page":"56","volume-title":"International conference on intelligent systems for molecular biology, Bethesda, MD","author":"A Califano","year":"1993","unstructured":"Califano A, Rigoutsos I: FLASH: a fast look-up algorithm for string homology. International conference on intelligent systems for molecular biology, Bethesda, MD 1993, 56\u201364."},{"key":"3200_CR17","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1016\/j.jpdc.2006.10.002","volume":"67","author":"PD Michailidis","year":"2007","unstructured":"Michailidis PD, Margaritis KG: A programmable array processor architecture for flexible approximate string matching algorithms. J Parallel Distrib Comput 2007, 67: 131\u2013141.","journal-title":"J Parallel Distrib Comput"},{"key":"3200_CR18","doi-asserted-by":"publisher","first-page":"656","DOI":"10.1101\/gr.229202. Article published online before March 2002","volume":"12","author":"WJ Kent","year":"2002","unstructured":"Kent WJ: BLAT: the BLAST-like alignment tool. Genome Research 2002, 12: 656\u2013664.","journal-title":"Genome Research"},{"key":"3200_CR19","volume-title":"Fourth IEEE symposium on bioinformatics and bioengineering (BIBE'04), Taichung, Taiwan","author":"HP Lee","year":"2004","unstructured":"Lee HP, Tsai YT, Sheu TF, Tang CT: An IDC-based algorithm for efficient homology filtration with guaranteed seriate coverage. Fourth IEEE symposium on bioinformatics and bioengineering (BIBE'04), Taichung, Taiwan 2004."},{"key":"3200_CR20","first-page":"553","volume-title":"IEEE Computer Society Bioinformatics Conference (CSB'03)","author":"Hong Sun","year":"2003","unstructured":"Sun Hong, Ozturk Ozgur, Ferhatosmanoglu Hakan: CoMRI: A Compressed Multi-Resolution Index Structure for Sequence Similarity Queries. IEEE Computer Society Bioinformatics Conference (CSB'03) 2003, 553."},{"key":"3200_CR21","first-page":"359","volume-title":"Proc of IEEE Sym on Bioinformatics and Bioengineering","author":"O Ozturk","year":"2003","unstructured":"Ozturk O, Ferhatosmanoglu H: Effective Indexing and Filtering for Similarity Search in Large Biosequence Databases. Proc of IEEE Sym on Bioinformatics and Bioengineering 2003, 359\u2013366."},{"key":"3200_CR22","first-page":"1","volume-title":"IPDPS 2007","author":"T Oliver","year":"2007","unstructured":"Oliver T, Yeow LY, Schmidt B: High Performance Database Searching with HMMer on FPGAs. IPDPS 2007 2007, 1\u20137."},{"key":"3200_CR23","doi-asserted-by":"publisher","first-page":"342","DOI":"10.1016\/j.jcss.2004.12.003","volume":"70","author":"Jeremy Buhler","year":"2005","unstructured":"Buhler Jeremy, Keich Uri, Sun Yanni: Designing seeds for similarity search in genomic DNA. Journal of Computer and System Sciences 2005, 70: 342\u2013363.","journal-title":"Journal of Computer and System Sciences"},{"key":"3200_CR24","volume-title":"Nordic Journal of Computing","author":"Veli Makinen","year":"2005","unstructured":"Makinen Veli, Navarro Gonzalo: Succinct suffix arrays based on run-length encoding. Nordic Journal of Computing 2005."},{"key":"3200_CR25","first-page":"164","volume":"14","author":"L Ming","year":"2003","unstructured":"Ming L, Bin M, Derek K, John T: PatternHuter II: Highly Sensitive and Fast Homology Search. Genome Informatics 2003, 14: 164\u2013175.","journal-title":"Genome Informatics"},{"key":"3200_CR26","first-page":"39","volume-title":"Proceedings of the 7th International Symposium on String Processing and Information Retrieval","author":"L Bergroth","year":"2000","unstructured":"Bergroth L, Hakonen H, Raita T: A survey of longest common subsequence algorithms. Proceedings of the 7th International Symposium on String Processing and Information Retrieval 2000, 39\u201348."},{"key":"3200_CR27","doi-asserted-by":"publisher","first-page":"10915","DOI":"10.1073\/pnas.89.22.10915","volume":"89","author":"S Henikoff","year":"1992","unstructured":"Henikoff S, Henikoff JG: Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci 1992, 89: 10915\u201310919.","journal-title":"Proc Natl Acad Sci"},{"key":"3200_CR28","volume-title":"Bioinformatics Sequence and Genome Analysis","author":"DW Mount","year":"2001","unstructured":"Mount DW: Bioinformatics Sequence and Genome Analysis. Cold Spring Harbor Laboratory Press; 2001."},{"issue":"11","key":"3200_CR29","doi-asserted-by":"publisher","first-page":"1697","DOI":"10.1101\/gr.6435207","volume":"17","author":"JC Dohm","year":"2007","unstructured":"Dohm JC, Lottaz C, Borodina T, Himmelbauer H: SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Res 2007, 17(11):1697\u20131706.","journal-title":"Genome Res"},{"key":"3200_CR30","unstructured":"Maq[ http:\/\/maq.sourceforge.net\/index.shtml ]"},{"key":"3200_CR31","unstructured":"Human Genome Resources[ http:\/\/www.ncbi.nlm.nih.gov ]"},{"key":"3200_CR32","doi-asserted-by":"crossref","unstructured":"Karlin S, Altschul SF: Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc Natl Acad Sci 87: 2264\u20132268.","DOI":"10.1073\/pnas.87.6.2264"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-10-S1-S17.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-10-S1-S17\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-10-S1-S17.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,17]],"date-time":"2019-05-17T13:54:04Z","timestamp":1558101244000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-10-S1-S17"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,1]]},"references-count":32,"journal-issue":{"issue":"S1","published-print":{"date-parts":[[2009,1]]}},"alternative-id":["3200"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-10-s1-s17","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,1]]},"article-number":"S17"}}