ELIZA

return kwic search for used to out of >500 occurrences
298981 occurrences (No.78 in the rank) during 5 years in the PubMed. [no cache] 500 found

329) Inspired again by ergodic theory, the weightings of the nucleotide triplets obtained from our training procedure are used to define a probability distribution on finite sequences, which can be used to distinguish between intron and exon sequences from the human genome of lengths between 750 and 5,000 bp.

--- ABSTRACT ---

PMID:24448658 DOI:10.1007/s00285-014-0754-2

2015 Journal of mathematical biology

* Coding sequence density estimation via topological pressure.

- We give a new approach to coding sequence (CDS) density estimation in genomic analysis based on the topological pressure, which we develop from a well known concept in ergodic theory. Topological pressure measures the 'weighted information content' of a finite word, and incorporates 64 parameters which can be interpreted as a choice of weight for each nucleotide triplet. We train the parameters so that the topological pressure fits the observed coding sequence density on the human genome, and use this to give ab initio predictions of CDS density over windows of size around 66,000 bp on the genomes of Mus Musculus, Rhesus Macaque and Drososphilia Melanogaster. While the differences between these genomes are too great to expect that training on the human genome could predict, for example, the exact locations of genes, we demonstrate that our method gives reasonable estimates for the 'coarse scale' problem of predicting CDS density. Inspired again by ergodic theory, the weightings of the nucleotide triplets obtained from our training procedure are used to define a probability distribution on finite sequences, which can be used to distinguish between intron and exon sequences from the human genome of lengths between 750 and 5,000 bp. At the end of the paper, we explain the theoretical underpinning for our approach, which is the theory of Thermodynamic Formalism from the dynamical systems literature. Mathematica and MATLAB implementations of our method are available at http://sourceforge.net/projects/topologicalpres/ .

--- ABSTRACT END ---

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[frequency of next (right) word to used to]

(1)28 assess	(20)5 design	(39)3 establish	(58)2 find
(2)28 identify	(21)5 increase	(40)3 observe	(59)2 fit
(3)23 evaluate	(22)5 inform	(41)3 prevent	(60)2 form
(4)20 study	(23)5 obtain	(42)3 solve	(61)2 further
(5)17 estimate	(24)5 quantify	(43)3 validate	(62)2 gain
(6)17 measure	(25)5 reconstruct	(44)2 accurately	(63)2 help
(7)16 determine	(26)4 calculate	(45)2 address	(64)2 improve
(8)16 examine	(27)4 characterize	(46)2 amplify	(65)2 make
(9)12 explore	(28)4 confirm	(47)2 avoid	(66)2 match
(10)10 treat	(29)4 construct	(48)2 be	(67)2 optimize
(11)9 analyze	(30)4 illustrate	(49)2 conduct	(68)2 perform
(12)8 develop	(31)4 reduce	(50)2 create	(69)2 prepare
(13)8 investigate	(32)4 screen	(51)2 demonstrate	(70)2 produce
(14)8 predict	(33)4 simulate	(52)2 derive	(71)2 promote
(15)7 collect	(34)4 verify	(53)2 describe	(72)2 recruit
(16)7 compare	(35)3 classify	(54)2 distinguish	(73)2 represent
(17)7 test	(36)3 compute	(55)2 explain	(74)2 select
(18)6 analyse	(37)3 control	(56)2 extrapolate
(19)6 detect	(38)3 define	(57)2 facilitate

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--- WordNet output for used --- =>1.〜に慣れて, 2.用いられた, 中古の Overview of verb use The verb use has 6 senses (first 3 from tagged texts) 1. (603) use, utilize, utilise, apply, employ -- (put into service; make work or employ for a particular purpose or for its inherent or natural purpose; "use your head!"; "we only use Spanish at home"; "I can't use this tool"; "Apply a magnetic field here"; "This thinking was applied to many projects"; "How do you utilize this tool?"; "I apply this rule to get good results"; "use the plastic bags to store the food"; "He doesn't know how to use a computer") 2. (12) use, habituate -- (take or consume (regularly or habitually); "She uses drugs rarely") 3. (8) use, expend -- (use up, consume fully; "The legislature expended its time on school questions") 4. use -- (seek or achieve an end by using to one's advantage; "She uses her influential friends to get jobs"; "The president's wife used her good connections") 5. practice, apply, use -- (avail oneself to; "apply a principle"; "practice a religion"; "use care when going down the stairs"; "use your common sense"; "practice non-violent resistance") 6. use -- (habitually do something (use only in the past tense); "She used to call her mother every week but now she calls only occasionally"; "I used to get sick when I ate in that dining hall"; "They used to vacation in the Bahamas") Overview of adj used The adj used has 3 senses (first 3 from tagged texts) 1. (4) used -- (employed in accomplishing something; "the principle of surprise is the most used and misused of all the principles of war"- H.H.Arnold & I.C.Eaker) 2. (1) exploited, ill-used, put-upon, used, victimized, victimised -- (of persons; taken advantage of; "after going out of his way to help his friend get the job he felt not appreciated but used") 3. (1) secondhand, used -- (previously used or owned by another; "bought a secondhand (or used) car") --- WordNet end ---