CN103235902A - Prediction method for ribose nucleic acid (RNA) structure comprising false knots - Google Patents
Prediction method for ribose nucleic acid (RNA) structure comprising false knots Download PDFInfo
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Abstract
The invention discloses a prediction method for a ribose nucleic acid (RNA) structure comprising false knots. The method comprises the steps of determining all structural units in a to-be-predicted RNA sequence including the false knots, placing all known existing structural units in a structural unit pool S0={s1, s2, s3,...sn}, enabling n to be a structural unit sum, and enabling sn to represent an nth structural unit; determining U={U1, U2,..., Ur, ..., UR} by iteration, enabling Ur to represent an RNA structure obtained by iteration in an rth time with small RNA structure energy, and enabling R to be total iteration times; respectively determining similar values of every element in Ur and an actual RNA structure according to free energy of every element in Ur and the sum of occurrence frequency of every element in all RNA structures; and enabling an element with a high similar value in U to be predicted as the RNA structure of the to-be-predicted RNA sequence. According to the prediction method, prediction time of the RNA structure and space complexity can be reduced, and prediction sensitivity and specificity are improved.
Description
Technical field
The invention belongs to biological information engineering field, relate to a kind of forecast method of carrying out to RNA (ribonucleic acid) (hereinafter, abbreviating RNA as), relate in particular to the RNA structure prediction method that comprises false knot.
Background technology
False knot (pseudoknot also claims pseudo-knot) is the nucleic acid tertiary structure that comprises at least two loop-stem structures, and wherein, half of one of two stem rings is inserted between the two halves of another stem ring.Nineteen eighty-two has been found false knot first in Brassica 2 et 4 (turnip yellow mosaic virus).False knot is folded into the 3 D stereo conformation of knot shape, but is not real topology knot.
In fact, in advance the general considerations of the minimum free energy RNA structure of measuring tape false knot has been proved to be np complete problem.Yet many important biological methods depend on the prediction to the RNA structure of band false knot.For example, telomerase RNA component (Telomerase RNA component is with reference to figure 1) comprises its active vital false knot.Many viruses are used the false knot structure to form similar tRNA motif (tRNA-like motif) and are penetrated into host cell.Having widely, the RNA molecule of tertiary structure often has a large amount of false knots.
Yet, because the context sensitivity (context-sensitivity) of false knot structure or the characteristic of " overlapping " are difficult to that it is carried out biological computation and detect.The base pairing of false knot is well not nested, in other words, and the base-pair appearance that in sequence, overlaps each other.This makes the standard method (standard method of dynamic programming) of existing dynamic programming be difficult to the false knot sequence in the default RNA (ribonucleic acid) (hereinafter, abbreviating RNA as).The newer stochastic context method (method of stochastic context-free grammars) that has nothing to do has also run into same problem.In secondary structure prediction methods such as more popular Mfold and Pfold, the false knot structure that exists in the RNA sequence that even can not go to predict.
Therefore, how as far as possible raising is a science difficult problem that needs to be resolved hurrily to susceptibility and the specificity of the prediction of the RNA structural series of band false knot.
Summary of the invention
One of technical matters to be solved by this invention is to provide a kind of RNA structure to comprising false knot that can reduce time and space complexity to carry out forecast method.
In order to solve the problems of the technologies described above, the invention provides a kind of RNA structure prediction method that comprises false knot.This method comprises: step S10, determine all structural units in the RNA sequence to be predicted, and comprise false knot, the structural unit of all known existence is put into structural unit pond S
0={ s
1, s
2, s
3... s
n, n is the structural unit sum, s
nRepresent n structural unit; Step S20 based on all structural units in the RNA sequence to be predicted, determines U={ U by iteration
1, U
2..., U
r..., U
R, U
rRepresent the less RNA structure of RNA structural energy that the r time iteration obtains, R is total iterations; Step S30 is according to U
rIn each element free energy and in the RNA structure summation of the structural unit frequency of occurrences, determine U respectively
rIn the similar value of each element and actual RNA structure; Step S40, the element that similar value among the U is high is predicted as the RNA structure of this RNA sequence to be predicted.
Wherein, described based on all structural units in the RNA sequence to be predicted, determine U={ U by iteration
1, U
2..., U
r..., U
RStep, further comprise: substep S201, to structural unit U
rCompose null value, U
rRepresent the folding RNA structure that obtains the r time; K is initialized as 1 with iterations; Substep S202 carries out K time by substep S203 to substep S204 and folds processing; Substep S203 judges the structural unit s among the S one by one
iWhether can make current RNA structure U
rFree energy reduce and s
iWith U
rIn structural unit not overlapping, if be judged as and be, K=K+1 then is with s
iIncorporate U into
r, return substep S202 then folding next time, otherwise, if be judged as not, then continue to judge the s among the S
I+1Whether can make current RNA structure U
rFree energy reduce and s
iWith U
rIn structural unit not overlapping, up to all elements among the S is judged; Substep S204 if all elements among the S is judged, has not existed among the expression S and can reduce RNA structure U
rThe structural unit of free energy, then this iteration finishes.
Further, described substep S203 utilizes following expression formula to calculate current RNA structure U
rFree energy:
E=E
pseudo+E
nest，
E
Nest=E
Multiloop+ E
Stem+ E
Bulge+ E
Interloop+ E
Hairpin+ E
A, wherein,
E represents the free energy of RNA structure; E
NestThe energy of nested structure in the expression RNA structure, E
MultiloopBe the energy of multi-branched ring in the RNA structure, E
StemBe the energy in stem district in the RNA structure, E
BulgeBe the energy of RNA structure protrusions, E
InterloopBe the energy of interior ring in the RNA structure, E
HairpinBe the energy of hair fastener ring in the RNA structure, E
AThe compensation that is each structural unit connects parameter; E
PseudoThe energy of false knot in the expression RNA structure.
Further, calculate RNA structure U by following expression
rThe energy of middle false knot:
E
pseudo=A
1S
b+A
2P
b+A
3N
b+A
4+A
5
A
1Be the energy value that produces a false knot structure neutron false knot, S
bBe the number of false knot structure neutron false knot, P
bBe the pairing base-pair number on the false knot inner boundary, N
bBe the inner unpaired base number of false knot, A
2, A
3Be respectively P
bAnd N
bEnergy value, can be measured A by experiment
4Be the coaxial stacking energy weights in the false knot, A
5Be the connection parameter between the RNA structural unit, connect parameter and represent the modified value that is connected between RNA false knot and the RNA structural unit.
Preferably, among the step S30, calculate the similar value of each element and actual RNA structure among the U according to following formula:
Function(U
r)=E(U
r)×a/n+P(U
r)×b+c,r∈[1,k]
Wherein,
Function (U
r) expression U
rSimilar value with actual RNA structure;
E (U
r) expression structural unit U
rFree energy;
A, b, c, k are constants;
N represents RNA base sequence length;
P (U
r) expression U
rIn the summation of structural unit frequency of occurrences in the RNA structure.
Preferably, a ∈ [5,15], b ∈ [1,8], c ∈ [1,10], k ∈ [90,110].Optimally, a=10, b=3, c=5, k=100.
Compared with prior art, one or more embodiment of the present invention can have following advantage:
In the present invention, proposed to comprise the Forecasting Methodology of the RNA structure of false knot, this method is by utilizing hereinafter with the approximate data that describes in detail, can improve the RNA structure prediction accuracy that comprises false knot preferably, improve specificity and the susceptibility of prediction, prediction RNA structure is conformed to or close with practical structures.
In addition, this invention can not only be predicted the RNA secondary structure, even also has specificity and susceptibility preferably aspect the prediction RNA tertiary structure.
Other advantages of the present invention, target, to set forth in the following description to a certain extent with feature, and to a certain extent, based on being apparent to those skilled in the art to investigating hereinafter, perhaps can obtain instruction from the practice of the present invention.Target of the present invention and other advantages can be passed through following instructions, claims, and the specifically noted structure realizes and obtains in the accompanying drawing.
Description of drawings
Accompanying drawing is used to provide further understanding of the present invention, and constitutes the part of instructions, is used for jointly explaining the present invention with embodiments of the invention, is not construed as limiting the invention.In the accompanying drawings:
Fig. 1 is telomerase RNA component structure synoptic diagram;
Fig. 2 A illustrates the process flow diagram of structure that method is according to an embodiment of the invention determined the RNA of band false knot;
Fig. 2 B illustrates the process flow diagram of the detailed step of step S20 among Fig. 2 A;
Fig. 3 is time complexity and the space complexity comparison diagram that the inventive method and Pknots technology are preset these several RNA structures of mottle virus, mosaic virus, ingspot virus and sapiens mRNA;
Fig. 4 be the inventive method and ILM technology, MWM technology, Pknots technology respectively to multiple RNA sequence (HIV-1-RT, DR7741, TYMV, BMV1, TMV-3 '-up, TMV-3 '-down, HDV, Anti-HDV) when predicting, the prediction effect comparison diagram aspect susceptibility, specificity two.
Embodiment
Describe embodiments of the present invention in detail below with reference to drawings and Examples, how the application technology means solve technical matters to the present invention whereby, and the implementation procedure of reaching technique effect can fully understand and implements according to this.Need to prove that only otherwise constitute conflict, each embodiment among the present invention and each feature among each embodiment can mutually combine, formed technical scheme is all within protection scope of the present invention.
In addition, can in the computer system such as one group of computer executable instructions, carry out in the step shown in the process flow diagram of accompanying drawing, and, though there is shown logical order in flow process, but in some cases, can carry out step shown or that describe with the order that is different from herein.
Illustrate that at first some are about the concept in false knot and stem district etc.False knot (pseudoknot) is as by intersecting the structure that base-pair constitutes, and is tertiary structure unit the most widely among the RNA, is complicated but stable RNA structure, and the plane false knot is false knot subclass the most widely.By contrast, the stem district is made of adjacent continuous base-pair.
Present embodiment utilizes following formula to determine the energy of a false knot:
E
pseudo=A
1S
b+A
2P
b+A
3N
b+A
4+A
5
A wherein
1Be the energy value that produces a false knot structure neutron false knot, can be measured by experiment.S
bIt is the number of false knot structure neutron false knot; P
bIt is the pairing base-pair number on the false knot inner boundary; N
bIt is the inner unpaired base number of false knot; A
2, A
3Be respectively P
bAnd N
bEnergy value, can be measured by experiment; A
4Be coaxial stacking energy (coaxial stacking) weights in the false knot, A
5Be the connection parameter that (comprises for example hair fastener ring, multi-branched ring, interior ring, projection, stem district etc.) between the RNA structural unit, measured by experiment.Connect parameter and represent the modified value that is connected between RNA false knot and the RNA structural unit, different RNA false knot structures may connect also difference of parameter.
Present embodiment can utilize following expression to determine the energy of nested structure:
E
nest=E
multiloop+E
stem+E
bulge+E
interloop+E
hairpin+E
A
E wherein
MultiloopBe the energy of multi-branched ring in the RNA structure, E
StemBe the energy in stem district in the RNA structure, E
BulgeBe the energy of RNA structure protrusions, E
InterloopBe the energy of interior ring in the RNA structure, E
HairpinBe the energy of hair fastener ring in the RNA structure, E
AThe compensation that is each structural unit connects parameter, can be determined by experiment.
Like this, present embodiment can utilize following expression to determine the gross energy (free energy) of a RNA structure:
E=E
pseudo+E
nest
Use which kind of expression formula to determine the false knot energy, be directly connected to susceptibility and the specificity of Forecasting Methodology.Above-mentioned expression formula in conjunction with following each step that will illustrate, can be improved susceptibility and the specificity of band false knot RNA prediction preferably.
Describe each step of structure of determining the RNA of band false knot according to present embodiment in detail below in conjunction with Fig. 2 A.
Step S10 determines all structural units in the RNA sequence to be predicted, comprises false knot, and the structural unit of all known existence is put into structural unit pond S
0={ s
1, s
2, s
3... s
n, n is the structural unit sum, s
nRepresent n structural unit.
Step S20 based on all structural units in the RNA sequence to be predicted, determines U={ U by iteration
1, U
2..., U
r..., U
R, U
rRepresent the less RNA structure of RNA structural energy that the r time iteration obtains, R is total iterations, U
0=Φ;
Step S30, according to the free energy of each element among the U and in all RNA structures the summation of the structural unit frequency of occurrences, determine the similar value of each element and actual RNA structure among the U respectively;
Step S40, the element that similar value among the U is high is predicted as the RNA structure of this RNA sequence to be predicted.
Describe each step of the r time iteration among the step S20 in detail below with reference to Fig. 2 B.
Step S201, initialization structure (tax empty set) U
r← Φ, U
rRepresent the folding RNA structure that obtains the r time; Iterations K is initialized as 1, K ← 1.
Step S202 carries out folding the processing K time by step S203 to S204, and the value of folding number of times K is different because of the different RNA base sequence, can arrange flexibly according to requirements such as susceptibility and time complexities.Carrying out K folding meaning is: reach steady state (SS) by folding RNA base sequence.Judge that whether folding times is above K time.
Step S203 judges the structural unit s among the S one by one
iWhether can make current RNA structure U
rFree energy reduce and s
iWith U
rIn structural unit not overlapping, namely whether make E (U
r∪ { s
i)＜E (U
r) and
If be judged as and be, K=K+1 then is with s
iIncorporate U into
r, i.e. U
r← U
r∪ { s
i, return step S202 then folding next time, otherwise, if be judged as not, then continue to judge the s among the S
I+1Whether can make current RNA structure U
rFree energy reduce and s
I+1With U
rIn structural unit not overlapping up to all elements among the S is judged.
Substep S204 if all elements among the S is judged, has not existed among the expression S and can reduce RNA structure U
rThe structural unit of free energy, then this iteration finishes.
Describe step S30 below in detail, according to the free energy of each element among the U and in all RNA structures the summation of the frequency of occurrences, determine the similar value of each element and actual RNA structure among the U respectively.
For example, can calculate the similar value of each element and actual RNA structure among the U according to following formula:
Function (U
r)=E (U
r) * a/n+P (U
r) * b+c, r ∈ [1, k], Function (U
r) expression U
rWith the similar value of actual RNA structure, above-mentioned expression formula can make the RNA structure U that the more high expression of functional value is pre-
rMore near practical structures.Wherein:
U
rRepresent the folding RNA structure that obtains the r time
E (U
r) expression structural unit U
rFree energy
A, b, c, k are constants, can be preferably a ∈ [5,15] among the present invention by measuring, b ∈ [1,8], c ∈ [1,10], k ∈ [90,110], more preferably.In Fig. 4 experiment, a=10; B=3; C=5; K=100.
N represents RNA base sequence length;
P (U
r) expression U
rIn the summation of structural unit frequency of occurrences in the RNA structure.
Above-mentioned expression formula formula can make when selecting final RNA structure, both considered the factor of free energy minimum, also consider simultaneously the frequency of occurrences of structural unit. in other words, if a structural unit occurs, can think that then this structural unit also probably also can appear in the final RNA structure in a plurality of Local Search results.
The method that we propose is studied various RNA structures as a kind of structural unit unification, according to the contribution of the probability that adds free energy that these structural units reduce and appearance in the RNA folding process as the RNA structure, predict the RNA structure.Through RNA structures such as for example mottle virus, the mosaic virus that comprise false knot, ringspot virus, sapiens mRNA, HIV-1-RT, DR7741 are predicted, higher forecasting efficiency and accuracy (with reference to figure 3 and Fig. 4) have been obtained.
Fig. 3 is time complexity and the space complexity comparison diagram that the inventive method and Pknots technology are preset these several RNA structures of mottle virus, mosaic virus, ingspot virus and sapiens mRNA, and n represents that n is the number of RNA sequence base among Fig. 3.As can be seen from Figure 3, the present invention has clear superiority at time complexity.Fig. 4 be the inventive method and ILM technology, MWM technology, Pknots technology respectively to multiple RNA sequence (HIV-1-RT, DR7741, TYMV, BMV1, TMV-3 '-up, TMV-3 '-down, HDV, Anti-HDV) when predicting, the prediction effect comparison diagram aspect susceptibility, specificity two.As can be seen from Figure 4, to compare ILM technology, MWM technology and Pknots technology aspect susceptibility and specificity all relative more excellent for method of the present invention.
Though the disclosed embodiment of the present invention as above, the embodiment that described content just adopts for the ease of understanding the present invention is not in order to limit the present invention.Technician in any the technical field of the invention; under the prerequisite that does not break away from the disclosed spirit and scope of the present invention; can do any modification and variation in the details of implementing that reaches in form; but scope of patent protection of the present invention still must be as the criterion with the scope that appending claims was defined.
Claims (7)
1. a RNA structure prediction method that comprises false knot is characterized in that, comprising:
Step S10 determines all structural units in the RNA sequence to be predicted, comprises false knot, and the structural unit of all known existence is put into structural unit pond S
0={ s
1, s
2, s
3... s
n, n is the structural unit sum, s
nRepresent n structural unit;
Step S20 based on all structural units in the RNA sequence to be predicted, determines U={ U by iteration
1, U
2..., U
r..., U
R, U
rRepresent the less RNA structure of RNA structural energy that the r time iteration obtains, R is total iterations;
Step S30 is according to U
rIn each element free energy and in the RNA structure summation of the structural unit frequency of occurrences, determine U respectively
rIn the similar value of each element and actual RNA structure;
Step S40, the element that similar value among the U is high is predicted as the RNA structure of this RNA sequence to be predicted.
2. method according to claim 1 is characterized in that, and is described based on all structural units in the RNA sequence to be predicted, determines U={ U by iteration
1, U
2..., U
r..., U
RStep, further comprise:
Substep S201 is to structural unit U
rCompose null value, U
rRepresent the folding RNA structure that obtains the r time; K is initialized as 1 with iterations;
Substep S202 carries out K time by substep S203 to substep S204 and folds processing;
Substep S203 judges the structural unit s among the S one by one
iWhether can make current RNA structure U
rFree energy reduce and s
iWith U
rIn structural unit not overlapping, if be judged as and be, K=K+1 then is with s
iIncorporate U into
r, return substep S202 then folding next time, otherwise, if be judged as not, then continue to judge the s among the S
I+1Whether can make current RNA structure U
rFree energy reduce and s
iWith U
rIn structural unit not overlapping, up to all elements among the S is judged;
Substep S204 if all elements among the S is judged, has not existed among the expression S and can reduce RNA structure U
rThe structural unit of free energy, then this iteration finishes.
3. method according to claim 2 is characterized in that, described substep S203 utilizes following expression formula to calculate current RNA structure U
rFree energy:
E=E
pseudo+E
nest，
E
Nest=E
Multiloop+ E
Stem+ E
Bulge+ E
Interloop+ E
Hairpin+ E
A, wherein,
E represents the free energy of RNA structure;
E
NestThe energy of nested structure in the expression RNA structure, E
MultiloopBe the energy of multi-branched ring in the RNA structure, E
StemBe the energy in stem district in the RNA structure, E
BulgeBe the energy of RNA structure protrusions, E
InterloopBe the energy of interior ring in the RNA structure, E
HairpinBe the energy of hair fastener ring in the RNA structure, E
AThe compensation that is each structural unit connects parameter;
E
PseudoThe energy of false knot in the expression RNA structure.
4. method according to claim 3 is characterized in that, calculates RNA structure U by following expression
rThe energy of middle false knot:
E
pseudo=A
1S
b+A
2P
b+A
3N
b+A
4+A
5
A
1Be the energy value that produces a false knot structure neutron false knot, S
bBe the number of false knot structure neutron false knot, P
bBe the pairing base-pair number on the false knot inner boundary, N
bBe the inner unpaired base number of false knot, A
2, A
3Be respectively P
bAnd N
bEnergy value, can be measured A by experiment
4Be the coaxial stacking energy weights in the false knot, A
5Be the connection parameter between the RNA structural unit, connect parameter and represent the modified value that is connected between RNA false knot and the RNA structural unit.
5. according to each described method in the claim 1 to 4, it is characterized in that, among the step S30, calculate the similar value of each element and actual RNA structure among the U according to following formula:
Function(U
r)=E(U
r)×a/n+P(U
r)×b+c,r∈[1,k]
Wherein,
Function (U
r) expression U
rSimilar value with actual RNA structure;
E (U
r) expression structural unit U
rFree energy;
A, b, c, k are constants;
N represents RNA base sequence length;
P (U
r) expression U
rIn the summation of structural unit frequency of occurrences in the RNA structure.
6. method according to claim 5 is characterized in that, a ∈ [5,15], b ∈ [1,8], c ∈ [1,10], k ∈ [90,110].
7. method according to claim 6 is characterized in that, a=10, b=3, c=5, k=100.
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| CN103235902B (en) | 2016-03-09 |
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