scholarly journals Seqpare: a self-consistent metric of similarity between genomic interval sets

2020 ◽  
Author(s):  
Selena C. Feng ◽  
Nathan C. Sheffield ◽  
Jianglin Feng
Keyword(s):  
Single Index ◽  
Link Type ◽  
Effective Metric ◽  
Genomic Interval ◽  
Self Consistent ◽  
Self Consistency

ABSTRACTSummarySearching genomic interval sets produced by sequencing methods has been widely and routinely performed; however, existing metrics for quantifying similarities among interval sets are inconsistent. Here we introduce Seqpare, a self-consistent and effective metric of similarity and tool for comparing sequences based on their interval sets. With this metric, the similarity of two interval sets is quantified by a single index, the ratio of their effective overlap over the union: an index of zero indicates unrelated interval sets, and an index of one means that the interval sets are identical. Analysis and tests confirm the effectiveness and self-consistency of the Seqpare metric.Availabilityhttps://github.com/deepstanding/[email protected]

scholarly journals Seqpare: a novel metric of similarity between genomic interval sets

F1000Research ◽  
2021 ◽  
Vol 9 ◽  
pp. 581
Author(s):  
Selena C. Feng ◽  
Nathan C. Sheffield ◽  
Jianglin Feng
Keyword(s):  
Single Index ◽  
Effective Metric ◽  
Genomic Interval ◽  
Self Consistent ◽  
Self Consistency

Searching genomic interval sets produced by sequencing methods has been widely and routinely performed; however, existing metrics for quantifying similarities among interval sets are inconsistent. Here we introduce Seqpare, a self-consistent and effective metric of similarity and tool for comparing sequences based on their interval sets. With this metric, the similarity of two interval sets is quantified by a single index, the ratio of their effective overlap over the union: an index of zero indicates unrelated interval sets, and an index of one means that the interval sets are identical. Analysis and tests confirm the effectiveness and self-consistency of the Seqpare metric.

scholarly journals Seqpare: a self-consistent metric of similarity between genomic interval sets

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 581 ◽  
Author(s):  
Selena C. Feng ◽  
Nathan C. Sheffield ◽  
Jianglin Feng
Keyword(s):  
Single Index ◽  
Effective Metric ◽  
Genomic Interval ◽  
Self Consistent ◽  
Self Consistency

Searching genomic interval sets produced by sequencing methods has been widely and routinely performed; however, existing metrics for quantifying similarities among interval sets are inconsistent. Here we introduce Seqpare, a self-consistent and effective metric of similarity and tool for comparing sequences based on their interval sets. With this metric, the similarity of two interval sets is quantified by a single index, the ratio of their effective overlap over the union: an index of zero indicates unrelated interval sets, and an index of one means that the interval sets are identical. Analysis and tests confirm the effectiveness and self-consistency of the Seqpare metric.

scholarly journals Self-consistent treatment of v-groove quantum wire band structure in no parabolic approximation

2004 ◽  
Vol 1 (3) ◽  
pp. 69-77 ◽  
Author(s):  
Jasna Crnjanski ◽  
Dejan Gvozdic
Keyword(s):  
Band Structure ◽  
Quantum Wire ◽  
The Self ◽  
Flat Band ◽  
Band Model ◽  
Parabolic Approximation ◽  
Self Consistent ◽  
Band Absorption ◽  
Consistent Treatment ◽  
Self Consistency

The self-consistent no parabolic calculation of a V-groove-quantum-wire (VQWR) band structure is presented. A comparison with the parabolic flat-band model of VQWR shows that both, the self-consistency and the nonparabolicity shift sub band edges, in some cases even in the opposite directions. These shifts indicate that for an accurate description of inter sub band absorption, both effects have to be taken into the account.

CURRENTS, SPIN DENSITIES AND MEAN-FIELD FORM FACTORS IN ROTATING NUCLEI: A SEMI-CLASSICAL APPROACH

2004 ◽  
Vol 13 (01) ◽  
pp. 225-233 ◽  
Author(s):  
J. BARTEL ◽  
K. BENCHEIKH ◽  
P. QUENTIN
Keyword(s):  
Mean Field ◽  
Form Factors ◽  
Spin Vector ◽  
Self Consistent ◽  
Field Form ◽  
Local Densities ◽  
The Mean ◽  
Self Consistency ◽  
Spin Densities ◽  
Rotating Nuclei

We present self-consistent semi-classical local densities characterising the structure of rotating nuclei. A particular emphasis is put on those densities which are generated by the breaking of time-reversal symmetry through the cranking piece of the Routhian, namely the current density and the spin vector density. Our approach which is based on the Extended-Thomas-Fermi method goes beyond the Inglis cranking approach and contains naturally the Thouless-Valatin self-consistency terms expressing the response of the mean field to the time-odd part of the density matrix.

scholarly journals The Arctic Ocean Multi-Year Ice Balance, 1979-82

1990 ◽  
Vol 14 ◽  
pp. 252-255 ◽  
Author(s):  
D.A. Rothrock ◽  
D.R. Thomas
Keyword(s):  
Arctic Ocean ◽  
Open Water ◽  
Measurement Model ◽  
The Arctic ◽  
First Year ◽  
Independent Data ◽  
Self Consistent ◽  
Buoy Data ◽  
Parameter Values ◽  
Self Consistency

A method of determining the temporally varying “state” of the ice cover (the concentrations of three surface types: open water, first-year ice, and multi-year ice) is presented. The methodology is that of Kalman smoothing: a physical model and a measurement model are used to blend satellite passive microwave data and buoy data to give an optimal estimate of the ice state. The estimates are optimal only to the degree that model parameter values are known and assumptions about variances are met. Uncertainty about these values and assumptions, and lack of independent data with which to compare results,leaves self-consistency as the most important test of results. A four-year record (1979-82) of the estimated Arctic Ocean ice balance is presented and shown to be self-consistent. Results are discussed in terms of the Arctic multi-year ice balance, which may be an important factor in the interaction ofocean, sea ice and climate because of its relationship to the minimum summer ice extent. The estimated area of multi-year ice decreases each year, but the decrease is small and insignificant based on four years of results. Furthermore, the observed decrease may be due to instrument drift or changes in the multi-year ice signature.

Dynamically consistent magnetic fields produced by differential rotation

1987 ◽  
Vol 178 ◽  
pp. 521-534 ◽  
Author(s):  
D. R. Fearn ◽  
M. R. E. Proctor
Keyword(s):  
Magnetic Field ◽  
Velocity Field ◽  
Flow Field ◽  
Differential Rotation ◽  
Zonal Flow ◽  
Nonlinear Characteristic ◽  
Poloidal Magnetic Field ◽  
Self Consistent ◽  
Self Consistency ◽  
The Magnetic Field

We investigate the dynamical consequences of an axisymmetric velocity field with a poloidal magnetic field driven by a prescribed e.m.f. E. The problem is motivated by previous investigations of dynamically driven dynamos in the magnetostrophic range. A geostrophic zonal flow field is added to a previously described velocity, and determined by the requirement that Taylor's constraint (Taylor 1963) (guaranteeing dynamical self-consistency of the fields) be satisfied. Several solutions are exhibited, and it is suggested that self-consistent solutions can always be found to this ‘forced’ problem, whereas the usual α-effect dynamo formalism in which E is a linear function of the magnetic field leads to a difficult transcendentally nonlinear characteristic value problem that may not always possess solutions.

Self-Consistent Hole Motion and Spin Excitations in A Quantum Antiferromagnet

1989 ◽  
Vol 03 (12) ◽  
pp. 1913-1932 ◽  
Author(s):  
Z.B. Su ◽  
Y.M. Li ◽  
W.Y. Lai ◽  
L. Yu
Keyword(s):  
The Self ◽  
Spin Excitation ◽  
Spin Correlations ◽  
Local Distortion ◽  
Spin Excitations ◽  
Self Consistent ◽  
The Stability ◽  
The One ◽  
Quantum Antiferromagnet ◽  
Self Consistency

A new quantum Bogoliubov-de Gennes (BdeG) formalism is developed to study the self-consistent motion of holes and spin excitations in a quantum antiferromagnet within the generalized t-J model. On the one hand, the effects of local distortion of spin configurations and the renormalization of the hole motion due to virtual excitations of the distorted spin background are treated on an equal footing to obtain the hole wave function and its spectrum, as well as the effective mass for a propagating hole. On the other hand, the change of the spin excitation spectrum and the spin correlations due to the presence of dynamical holes are studied within the same adiabatic approximation. The stability of the hole states with respect to such changes justifies the self-consistency of the proposed formalism.

The band structure of aluminium III. A self-consistent calculation

1957 ◽  
Vol 240 (1222) ◽  
pp. 361-374 ◽  
Keyword(s):  
Band Structure ◽  
Electron Gas ◽  
Careful Consideration ◽  
Correlation Effects ◽  
Conduction Electrons ◽  
Hartree Fock ◽  
Exchange Effects ◽  
Self Consistent ◽  
Core Electrons ◽  
Self Consistency

The main feature of the present recalculation of the band structure is a careful consideration of the potential on which it is based. An effective potential acting on a conduction electron is defined intuitively so as to include the effects of correlation and exchange. This grafts the Bohm & Pines theory of a free-electron gas (Pines 1955) on to the Hartree—Fock treatment of the effect of the ion cores. Correlation and exchange effects among the conduction and ion-core electrons have been calculated, and the variation of the potential in the regions about half-way between the atoms has also been calculated and taken into account. Achieving self-consistency in the contribution to the potential due to the conduction electrons has not been difficult. Because of various approximations, including those in the potential, the calculated energy values are judged to be correct to about 0·03 Ry. The results are found to agree satisfactorily with the model of the band structure obtained in I by noting that the effective Fermi level for electrons and holes in the band structure may not be the same due to additional correlation effects.

scholarly journals TIME MACHINES: THE PRINCIPLE OF SELF-CONSISTENCY AS A CONSEQUENCE OF THE PRINCIPLE OF MINIMAL ACTION

1995 ◽  
Vol 04 (05) ◽  
pp. 557-580 ◽  
Author(s):  
A. CARLINI ◽  
V.P. FROLOV ◽  
M.B. MENSKY ◽  
I.D. NOVIKOV ◽  
H.H. SOLENG
Keyword(s):  
Interaction Potential ◽  
Hard Sphere ◽  
Action Principle ◽  
Natural Consequence ◽  
Classical Action ◽  
Minimal Action ◽  
Interacting Particle ◽  
Self Consistent ◽  
Time Machines ◽  
Self Consistency

We consider the action principle to derive the classical, nonrelativistic motion of a self-interacting particle in a 4D Lorentzian spacetime containing a wormhole and which allows the existence of closed time-like curves. For the case of a “hard-sphere” self-interaction potential we show that the only possible trajectories (for a particle with fixed initial and final positions and which traverses the wormhole once) minimizing the classical action are those which are globally self-consistent, and that the “principle of self-consistency” (originally introduced by Novikov) is thus a natural consequence of the “principle of minimal action.”

Self-consistency in the interaction of magnetized electrons and ordinarily polarized electromagnetic waves

1993 ◽  
Vol 49 (1) ◽  
pp. 41-50
Author(s):  
F. B. Rizzato
Keyword(s):  
Free Energy ◽  
Electromagnetic Waves ◽  
Hamiltonian Formalism ◽  
Critical Value ◽  
Average Density ◽  
The Self ◽  
Dynamical Interaction ◽  
Wave Dynamics ◽  
Self Consistent ◽  
Self Consistency

We use a Hamiltonian formalism to analyse the self-consistent wave–particle dynamical interaction involving magnetized electrons and ordinarily polarized electromagnetic waves. Considering first-harmonic cyclotron resonances, we show that there is a critical value of the electronic average density. For systems with lower than critical densities the saturation process is dictated by relativistic detuning effects, and wave dynamics may be disregarded. However, for systems with larger densities, saturation is governed by the available electromagnetic free energy, and the wave dynamics turns out to be essential.

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