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Since metagenomic data\nincludes sequence fragments (\u201creads\u201d) from organisms\nthat are absent from any database, new algorithms must be\ndeveloped for the identification and annotation of novel sequence\nfragments. Homology\u2010based techniques have been modified to detect\nnovel species and genera, but, composition\u2010based methods, have not\nbeen adapted. We develop a detection technique that can\ndiscriminate between \u201cknown\u201d and \u201cunknown\u201d\ntaxa, which can be used with composition\u2010based methods, as well as\na hybrid method. Unlike previous studies, we rigorously evaluate\nall algorithms for their ability to detect novel taxa.  First, we\nshow that the integration of a detector with a composition\u2010based\nmethod performs significantly better than homology\u2010based methods\nfor the detection of novel species and genera, with best\nperformance at finer taxonomic resolutions. Most importantly, we\nevaluate all the algorithms by introducing an\n\u201cunknown\u201d class and show that the modified version of\nPhymmBL has similar or better overall classification performance\nthan the other modified algorithms, especially for the\nspecies\u2010level and ultrashort reads. Finally, we evaluate the\nperformance of several algorithms on a real acid mine drainage\ndataset.<\/jats:p>","DOI":"10.1155\/2011\/495849","type":"journal-article","created":{"date-parts":[[2011,3,23]],"date-time":"2011-03-23T19:31:55Z","timestamp":1300908715000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Discovering the Unknown: Improving Detection of Novel  Species and Genera from Short Reads"],"prefix":"10.1155","volume":"2011","author":[{"given":"Gail L.","family":"Rosen","sequence":"first","affiliation":[]},{"given":"Robi","family":"Polikar","sequence":"additional","affiliation":[]},{"given":"Diamantino A.","family":"Caseiro","sequence":"additional","affiliation":[]},{"given":"Steven D.","family":"Essinger","sequence":"additional","affiliation":[]},{"given":"Bahrad A.","family":"Sokhansanj","sequence":"additional","affiliation":[]}],"member":"311","published-online":{"date-parts":[[2011,3,23]]},"reference":[{"key":"e_1_2_9_1_2","volume-title":"Committee on Metagenomics: Challenges and Functional Applications","author":"Handelsman J.","year":"2007"},{"key":"e_1_2_9_2_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1093857"},{"key":"e_1_2_9_3_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.5969107"},{"key":"e_1_2_9_4_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0001584"},{"key":"e_1_2_9_5_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth0909-636"},{"key":"e_1_2_9_6_2","unstructured":"EssingerS.andRosenG. 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