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Frequency analysis techniques for identification of viral genetic data


, : Frequency analysis techniques for identification of viral genetic data. Mbio 1(3): -

Environmental metagenomic samples and samples obtained as an attempt to identify a pathogen associated with the emergence of a novel infectious disease are important sources of novel microorganisms. The low costs and high throughput of sequencing technologies are expected to allow for the genetic material in those samples to be sequenced and the genomes of the novel microorganisms to be identified by alignment to those in a database of known genomes. Yet, for various biological and technical reasons, such alignment might not always be possible. We investigate a frequency analysis technique which on one hand allows for the identification of genetic material without relying on alignment and on the other hand makes possible the discovery of nonoverlapping contigs from the same organism. The technique is based on obtaining signatures of the genetic data and defining a distance/similarity measure between signatures. More precisely, the signatures of the genetic data are the frequencies of k-mers occurring in them, with k being a natural number. We considered an entropy-based distance between signatures, similar to the Kullback-Leibler distance in information theory, and investigated its ability to categorize negative-sense single-stranded RNA (ssRNA) viral genetic data. Our conclusion is that in this viral context, the technique provides a viable way of discovering genetic relationships without relying on alignment. We envision that our approach will be applicable to other microbial genetic contexts, e.g., other types of viruses, and will be an important tool in the discovery of novel microorganisms.

US$19.90

PMID: 20824103

DOI: 10.1128/mBio.00156-10


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Sureja, D.K.; Dholakia, S.P.; Vadalia, K.R., 2017: Synthesis of some novel pyrazolo[3,4-id ] pyrimidin-4(5iH )-one derivatives as potential antimicrobial agent. The aim of the present work was to synthesize a novel series of pyrazolo[3,4-<i>d</i>]pyrimidin-4(5<i>H</i>)-one derivatives and evaluate their <i>in vitro</i> antimicrobial activity. Cyclization of an ortho-ami...

Brownstein, D.G., 1987: Tracheal mucociliary transport in laboratory mice: evidence for genetic polymorphism. Mean tracheal transport velocities of inhaled 3.mu. coumarin-bound monodisperse latex spheres, measured by epi-fluorescence through the intact trachea of anesthetized mice, were 2.29 .+-. 0.52 mm/min for C57BL/6J, 0.40 .+-. 0.42 mm/min for DBA/2J...

Ohta, H.; Kosumi, T.; Kitai, T.; Yamamoto, S.; Ukikusa, M.; Awane, H.; Shintaku, M., 1997: Three patients with bilateral breast tumors examined by technetium-99m-sestamibi scintimammography. We presented three patients with bilateral breast tumors (one with breast cancers, one with breast cancer and fibroadenoma, and one with fibroadenomas) examined by 99mTc-hexakis 2-methoxy-isobutylisonitrile (MIBI) scintimammography. In all cases 9...

Nikiforova N.M.; Kedrova T.V.; Naumov S.V., 2000: Express method to study heavy fraction of diamond-bearing region. Metallogeniya Drevnikh i Sovremennykh Okeanov : erialy ... Nauchnoy Studencheskoy Shkoly. 6; Pages 291. 2000.

Kim, E.Young.; Choi, J.Seok.; Lee, K.Eun.; Kim, C.Seong.; Bae, E.Hui.; Ma, S.Kwon.; Kim, S.Hee.; Lee, J.Un.; Kim, S.Wan., 2012: Altered regulation of renal Acid base transporters in response to ammonium chloride loading in rats. The role of the kidney in combating metabolic acidosis has been a subject of considerable interest for many years. The present study was aimed to determine whether there is an altered regulation of renal acid base transporters in acute and chronic...

Shimada, K.; Miyauchi, K.; Mokuno, H.; Miyazaki, T.; Seki, E.; Watanabe, Y.; Iwama, Y.; Shigekiyo, M.; Matsumoto, M.; Okazaki, S.; Tanimoto, K.; Kawamura, M.; Suzuki, H.; Kurata, T.; Sato, H.; Daida, H., 2002: Predictive value of the adipocyte-derived plasma protein adiponectin for restenosis after elective coronary stenting. The purpose of this study was to test the hypothesis that plasma levels of adiponectin can predict angiographic in-stent restenosis after coronary stenting. We prospectively examined adiponectin levels in 127 consecutive patients undergoing electi...

Todorić, M.; Cvorović, N.; Ilić, R.; Simić, A.; Kronja, G.; Jablanov, J., 1994: Arterial embolism caused by penetration and migration of a bullet through the thoracic aorta. Vojnosanitetski Pregled 51(1): 65-69

Lecompte, Y.; Franco, D.; Martin, E.D.; Bismuth, H., 1974: Liver arterialization with portacaval shunt in the cirrhotic rat. Surgery 75(2): 161-168

Leguerrier A.M.; Allannic H.; Fauchet R.; Lorcy Y.; Guequen M.; Savath H.P.; Genetet B., 1984: Genetic markers and graves disease study of complement c 4 alleles. Journal of Steroid Biochemistry 20(6 PART B): 1647

Simon, A.; Satyanarayana, S.V.M., 2012: Steady state dynamics of a moving model cell. Crawling cell motility results due to treadmilling of a polymerized actin network at the leading edge. Steady state dynamics of a moving cell are governed by actin concentration profiles across the cell. Branching of new filaments implicating Arp2...