{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T06:04:11Z","timestamp":1791180251474,"version":"4.1.0"},"reference-count":23,"publisher":"American Association for the Advancement of Science (AAAS)","issue":"5575","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Science"],"published-print":{"date-parts":[[2002,6,14]]},"abstract":"<jats:p>\n            Comparison of the whole-genome sequence of\n            <jats:italic>Bacillus anthracis<\/jats:italic>\n            isolated from a victim of a recent bioterrorist anthrax attack with a reference reveals 60 new markers that include single nucleotide polymorphisms (SNPs), inserted or deleted sequences, and tandem repeats. Genome comparison detected four high-quality SNPs between the two sequenced\n            <jats:italic>B. anthracis<\/jats:italic>\n            chromosomes and seven differences among different preparations of the reference genome. These markers have been tested on a collection of anthrax isolates and were found to divide these samples into distinct families. These results demonstrate that genome-based analysis of microbial pathogens will provide a powerful new tool for investigation of infectious disease outbreaks.\n          <\/jats:p>","DOI":"10.1126\/science.1071837","type":"journal-article","created":{"date-parts":[[2002,7,27]],"date-time":"2002-07-27T09:54:32Z","timestamp":1027763672000},"page":"2028-2033","source":"Crossref","is-referenced-by-count":339,"title":["Comparative Genome Sequencing for Discovery of Novel Polymorphisms in\n            <i>Bacillus anthracis<\/i>"],"prefix":"10.1126","volume":"296","author":[{"given":"Timothy D.","family":"Read","sequence":"first","affiliation":[{"name":"The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven L.","family":"Salzberg","sequence":"additional","affiliation":[{"name":"The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mihai","family":"Pop","sequence":"additional","affiliation":[{"name":"The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"Shumway","sequence":"additional","affiliation":[{"name":"The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lowell","family":"Umayam","sequence":"additional","affiliation":[{"name":"The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lingxia","family":"Jiang","sequence":"additional","affiliation":[{"name":"The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erik","family":"Holtzapple","sequence":"additional","affiliation":[{"name":"The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joseph D.","family":"Busch","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kimothy L.","family":"Smith","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James M.","family":"Schupp","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"Solomon","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul","family":"Keim","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claire M.","family":"Fraser","sequence":"additional","affiliation":[{"name":"The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"221","reference":[{"key":"e_1_3_1_2_2","unstructured":"Centers for Disease Control Morb. Mortal. Wkly. Rep. 50 877 (2001)."},{"key":"e_1_3_1_3_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.181.8.2358-2362.1999"},{"key":"e_1_3_1_4_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.182.10.2928-2936.2000"},{"key":"e_1_3_1_5_2","unstructured":"Centers for Disease Control Morb. Mortal. Wkly. Rep. 50 909 (2001)."},{"key":"e_1_3_1_6_2","unstructured":"The index strain was sent from Fort Detrick to Porton Down UK in or after 1982 and was cured of the pXO1 and pXO2 virulence plasmids (Fig. 1). Two preparations of genomic DNA were sent to TIGR. The first was prepared in a laboratory at the University of California Berkeley in 1998 (\u201cPorton1\u201d). The second was prepared at Porton Down in 2001 from a bacterium grown from the original frozen culture (\u201cPorton2\u201d). The reported history of storage of the bacteria used to create the cultures provides no obvious reasons for the seven intrastrain chromosomal SNPs observed (Table 1)."},{"key":"e_1_3_1_7_2","unstructured":"Materials and methods are available as supporting material on Science Online."},{"key":"e_1_3_1_8_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/27.11.2369"},{"key":"e_1_3_1_9_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.181.20.6509-6515.1999"},{"key":"e_1_3_1_10_2","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-2672.1999.00883.x"},{"key":"e_1_3_1_11_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.8.3.175"},{"key":"e_1_3_1_12_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.8.3.186"},{"key":"e_1_3_1_13_2","unstructured":"For a full discussion of quality value determinations see supporting material on Science Online."},{"key":"e_1_3_1_14_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid0703.017335"},{"key":"e_1_3_1_15_2","unstructured":"If a small portion of the genome has low coverage this will have a disproportionate effect on the overall accuracy for the genome. For example suppose that 10% of the genome has low coverage and an error rate of 1\/10 000 whereas 90% of the genome has an error rate of 1\/100 000 000. At a hypothetical average error rate per sequence of 1% (corresponding to a quality value of 20) 2-fold coverage will yield an error rate of 1\/10 000 whereas 4-fold coverage will have an error rate of 1\/100 000 000. This distribution would produce an overall sequencing accuracy of 1\/100 000 despite the fact that the accuracy for 90% of the genome was essentially perfect."},{"key":"e_1_3_1_16_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.184.1.134-141.2002"},{"key":"e_1_3_1_17_2","unstructured":"X. X. Peterson et al. in preparation."},{"key":"e_1_3_1_18_2","unstructured":"This deletion occurs in a complex repeat composed of four distinct units (labeled A to D). The order of these units in the Pasteur pXO2 plasmid is ACDCBACB followed by another copy of D about 4.3-kbp downstream. The Florida isolate plasmid lacks the 1.4-kbp region between the two extreme copies of the C unit leading to the ACB genotype."},{"key":"e_1_3_1_19_2","doi-asserted-by":"publisher","DOI":"10.1016\/0378-1119(86)90044-2"},{"key":"e_1_3_1_20_2","unstructured":"C. B. Thorne in Bacillus subtilis and Other Gram-Positive Bacteria (American Society for Microbiology Washington DC 1993) pp. 113\u2013124."},{"key":"e_1_3_1_21_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.184.3.621-628.2002"},{"key":"e_1_3_1_22_2","unstructured":"Regions surrounding selected SNPs were amplified by PCR and the products were sequenced. VNTRs were typed by sequencing and\/or sizing on acrylamide gels (3). In cases where the SNPs or VNTRs differed from the Florida strain sequence (asterisk in Table 4) two additional sequence reactions were performed in order to obtain better overall quality values and at least 3-fold coverage for each SNP tested."},{"key":"e_1_3_1_23_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0966-842X(99)01609-1"},{"key":"e_1_3_1_24_2","unstructured":"The sequencing of the Florida isolate was supported by National Science Foundation Small Grant for Exploratory Research (MCB-202304 to C.M.F. and T.D.R.). The Porton genome sequence was supported by a grant (N00149610604) from the Office of Naval Research which was supplemented by the NIH Department of Energy (grant DEFC0295ER6196) and funds from the United Kingdom Defence Science Technology Laboratory. S.L.S and M.P. were supported in part by NSF (grant KDI-9980088) and NIH (grant R01-LM06845). Supporting Online Material www.sciencemag.org\/cgi\/content\/full\/1071837\/DC1 Materials and Methods Table S1"}],"container-title":["Science"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.science.org\/doi\/pdf\/10.1126\/science.1071837","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,1,10]],"date-time":"2024-01-10T03:40:47Z","timestamp":1704858047000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.science.org\/doi\/10.1126\/science.1071837"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2002,6,14]]},"references-count":23,"journal-issue":{"issue":"5575","published-print":{"date-parts":[[2002,6,14]]}},"alternative-id":["10.1126\/science.1071837"],"URL":"https:\/\/doi.org\/10.1126\/science.1071837","relation":{},"ISSN":["0036-8075","1095-9203"],"issn-type":[{"value":"0036-8075","type":"print"},{"value":"1095-9203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2002,6,14]]}}}