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Moving along the genome of a query sequence in a sliding window, the BI computes a ratio quantifying how closely the query sequence clusters with a subtype clade. In its current version, however, the BI does not provide predicted boundaries of unknown fragments.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We have developed <jats:italic>Unknown Subtype Finder<\/jats:italic> (USF), an algorithm based on a probabilistic model, which automatically determines which parts of an input sequence originate from a subtype yet unknown. The underlying model is based on a simple profile hidden Markov model (pHMM) for each <jats:italic>known<\/jats:italic> subtype and an additional pHMM for an <jats:italic>unknown<\/jats:italic> subtype. The emission probabilities of the latter are estimated using the emission frequencies of the known subtypes by means of a (position-wise) probabilistic model for the emergence of new subtypes. We have applied USF to SIV and HIV-1 sequences formerly classified as having emerged from an unknown subtype. Moreover, we have evaluated its performance on artificial HIV-1 recombinants and non-recombinant HIV-1 sequences. The results have been compared with the corresponding results of the BI.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>Our results demonstrate that USF is suitable for detecting segments in HIV-1 sequences stemming from yet unknown subtypes. Comparing USF with the BI shows that our algorithm performs as good as the BI or better.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-12-93","type":"journal-article","created":{"date-parts":[[2011,4,12]],"date-time":"2011-04-12T18:54:11Z","timestamp":1302634451000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":19,"title":["Detection of viral sequence fragments of HIV-1 subfamilies yet unknown"],"prefix":"10.1186","volume":"12","author":[{"given":"Thomas","family":"Unterthiner","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anne-Kathrin","family":"Schultz","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jan","family":"Bulla","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Burkhard","family":"Morgenstern","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mario","family":"Stanke","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ingo","family":"Bulla","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2011,4,11]]},"reference":[{"key":"4471_CR1","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1093\/bmb\/58.1.19","volume":"58","author":"B Korber","year":"2001","unstructured":"Korber B, Gaschen B, Yusim K, Thakallapally R, Kesmir C, Detours V: Evolutionary and immunological implications of contemporary HIV-1 variation. 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