CN104298894A - Prediction method and device for RNA false knot structure based on k stems - Google Patents

Abstract

The invention provides a prediction method and device for an RNA false knot structure based on k stems. The prediction method comprises the following steps that a section of RNA base sequence is input, and false knots and k (k is larger than or equal to one) stems are defined; RNA bases and k stems are searched for from left to right, and all the found k stems are subjected to determined marking; the false knots are searched for according to the characteristic that the k stems intersect to form the false knots, and the minimum free energy of the RNA false knot structure including the k stems is calculated; the RNA false knot structure is output. According to the prediction method, the searching speed is high, the accuracy is high, and the sensibility, specificity and the like are better than that of other related algorithms such as a PKNOTS algorithm. The prediction method is more effective on the aspect of plane false knot prediction than the PKNOTS algorithm.

Description

Based on Forecasting Methodology and the device of the RNA (ribonucleic acid) pseudoknot structure of k stem

Technical field

The invention belongs to biological information engineering field, relate to a kind of method that the pseudoknot structure of RNA (ribonucleic acid) (hereinafter referred to as RNA) is predicted, particularly relate to method and device that the RNA pseudoknot structure based on k stem predicts.

Background technology

RNA is one of of paramount importance large molecule in biosystem, and it exercises several functions in vivo, is the template of synthetic protein.RNA secondary structure prediction is used for protein functional assays, is the basis of RNA Tertiary structure predictions.False knot (pseudoknot) is structural unit the most widely in RNA, and be very complicated and stable RNA structure, false knot has structure, catalysis and regulatory function in RNA molecule, is the key point of current RNA structure prediction research.

The method that RNA secondary structure prediction adopts mainly contains two kinds: what adopt in early days is sequence comparative analysis's method, namely compare for the primary structure playing identical biological function in different organism, the where the shoe pinches of the method is: the homologous sequence of many RNA molecule is difficult to obtain; Need a large amount of manpower, efficiency is lower, so main employing at present is minimum free energy metering method.

The theoretical foundation of minimum free energy quantity algorithm is that the free energy of stable RNA secondary structure is minimum.PKNOTS algorithm based on minimum free energy quantity algorithm uses O (n ⁶) time and O (n ⁴) space calculates arbitrary plane false knot and part on-plane surface false knot.PKNOTS algorithm only computational length can be shorter than the RNA sequence of 140 bases, can not meet the needs of longer RNA sequential structure prediction.PknotsRG algorithm calculates the simple nested false knot be made up of Liang Gejing district, and wherein any two false knots are arranged side by side or nest relation.In fact, by inner ring and the protruding false knot ubiquity in RNA formed, the false knot that intersects also has vital role.Therefore, both can not be left in the basket.Plane false knot is false knot subclass the most widely, comprises above-mentioned by inner ring and the protruding false knot formed and the situation of intersecting false knot.In all sequences of PseudoBase database, only a sequence is folded into an on-plane surface false knot, and all the other sequences are all folded into plane false knot.Therefore we mainly consider the calculating of arbitrary plane false knot.

Dynamic programming algorithm is used for being close to neighbor model most by Zuker first, propose MFOLD algorithm, updating and developing through two more than ten years, existing oneself becomes widely used RNA secondary structure prediction method in the world, for the RNA sequence comprising n nucleotide, MFOLD algorithm uses O (n ³) time and O (n ²) its optimum secondary structure of spatial prediction, at present length is less than to the RNA sequence of 700 general acid of core, MFOLD algorithm can the RNA base pair of correct Prediction about 73%, but can reduce for the prediction accuracy of long sequence and part subclass, this algorithm simply show the rough framework of Tertiary structure predictions, in addition due to the restriction of algorithm itself, MFOLD algorithm can not predict false knot and more complicated tertiary structure.

Summary of the invention

The technical matters that the present invention solves makes RNA structure prediction, especially carries out Forecasting Methodology to the RNA structure comprising false knot based on k stem, reduces time complexity and the space complexity of prediction, improve forecasting accuracy.

The Forecasting Methodology of a kind of RNA (ribonucleic acid) pseudoknot structure based on k stem that the present invention relates to comprises the following steps:

Input one section of ribonucleic acid base sequence;

Definition false knot, k stem, k >=1;

Search base and k stem from left to right, all k stems found out are marked;

Intersection according to two or more k stem base-pair forms pseudoknot structure characteristic, searches false knot;

Calculate the least energy of the RNA (ribonucleic acid) pseudoknot structure comprising k stem;

Export the pseudoknot structure of RNA (ribonucleic acid).

1 stem (is designated as S ₁[i, j]) by base-pair (i, j) with (r, s) ∈ S close, if (k-1) stem by base-pair (r ', s ') and (k, l) ∈ S close, i<r<r ' <k<l<s ' <s<j, v=r ’ – r+s-s ' >2, then by (i, j) and (k, l) ∈ S the structure closed be called that k stem (is designated as S _k[i, j]).Wherein, in two k stems, the intersection of base-pair forms false knot.When searching base from left to right, first search 1 stem, if find 1 stem, then to all kilobase marker in 1 stem, in like manner, search 2 stems, 3 stems ... k stem, if find, then to all kilobase marker in k stem.

A kind of prediction unit of the RNA (ribonucleic acid) pseudoknot structure based on k stem comprises:

Input block: it inputs one section of ribonucleic acid base sequence;

Definition unit: define 1 stem, 2 stems ... k stem;

Search unit: search base from left to right, to all 1 stems, 2 stems that find out ... base in k stem marks;

Pseudoknot structure searches unit: the intersection according to two or more k stem base-pair forms pseudoknot structure characteristic, searches false knot;

False knot computing unit: the least energy calculating the RNA (ribonucleic acid) pseudoknot structure comprising k stem;

Output unit: it is according to least-energy principle, exports the pseudoknot structure of ribonucleic acid base sequence.

The search speed of method of the present invention, accuracy, Sensitivity and Specificity are all better than PKNOTS algorithm.Therefore this method is more effective than PKNOTS algorithm in the prediction of plane false knot.

Accompanying drawing explanation

Fig. 1 is the Forecasting Methodology process flow diagram of the RNA pseudoknot structure based on k stem of the present invention;

Fig. 2 is the process flow diagram of k stem of the present invention process;

Fig. 3 is for predicting the prediction unit of RNA pseudoknot structure in corresponding diagram 1;

Fig. 4 is the example of a RNA pseudoknot structure of the present invention;

Fig. 5 is the expression diagram of W and V in calculating RNA pseudoknot structure least energy of the present invention.

Embodiment

First concept about RNA sequence, base-pair, false knot etc. is described.

RNA primary structure: the expression that puts in order of four kinds of bases on RNA molecule side chain.In general RNA base sequence terminates to 3 ' from 5 ', and whole like this sequence s is expressed as s=s ₁s ₂s _n, s _irepresent i-th base of RNA sequence, s _i∈ { A, U, G, C}, RNA subsequence s _i,jbe a sequence fragment of s, be expressed as: s _i,j=s _is _j.

Base-pair: if s _is _j∈ { AU, CG, GU}, then s _is _jform base-pair.Energy stacking in base-pair is negative value.

RNA secondary structure: one group of base in RNA sequence, to the set formed, represents with S.For any base pair, if s _is _j∈ S, s _{i '}s _{j '}if ∈ S and i=i ', then j=j ', that is a base can not form base pair with two and plural base simultaneously.

False knot: if base is to s _is _jwith s _{i '}s _{j '}∈ S, if i < i ' < j < j ', then sequence s _i... s _{i '}... s _j...s _{j '}form pseudoknot structure.

Fig. 1 is according to the process flow diagram for predicting the Forecasting Methodology based on stem district RNA pseudoknot structure of the present invention; Method of the present invention comprises the following steps: input one section of RNA sequence; Definition false knot, k stem (k >=1); Search base from left to right, all k stems found out are marked; Intersection according to two or more k stem base-pair forms pseudoknot structure characteristic, searches false knot; Calculate the least energy of the RNA (ribonucleic acid) pseudoknot structure comprising k stem; Export the pseudoknot structure of RNA (ribonucleic acid).Fig. 3 is for predicting the prediction unit of the RNA pseudoknot structure based on stem district in corresponding diagram 1.The prediction unit of RNA pseudoknot structure comprises: input block: it inputs one section of ribonucleic acid base sequence; Definition unit: its definition false knot and definition k stem, k >=1; Search unit: search base from left to right, to all 1 stems, 2 stems that find out ... base in k stem marks; Pseudoknot structure searches unit: the intersection according to two or more k stem base-pair forms pseudoknot structure characteristic, searches false knot; False knot energy calculation unit: the least energy calculating the RNA (ribonucleic acid) pseudoknot structure comprising k stem; Output unit: it is according to least-energy principle, exports the pseudoknot structure of ribonucleic acid base sequence.

Fig. 2 is the process flow diagram according to k stem of the present invention process: input one section of s=s ₁s ₂s _nsequence, searches base from left to right, if there is i, j, makes s _iand s _jpairing, j-i>=6, and there are more than three the adjacent bases of continuous print in s to s _is _j, s _(i+1)s _(j-1).。。, s _ks _l, then base is to s _is _jand s _ks _lthe interval closed is defined as 1 stem; The base of pairings all in 1 stem is marked; The free base relaying closed at 1 stem continues the base of searching pairing, if there are more than three bases pair, is defined as 2 stems; The base of pairings all in 2 stems is marked; The free base relaying closed at 1 stem and 2 stems continues the base of searching pairing, if there are more than three bases pair, is defined as 3 stems; The base of pairings all in 3 stems is marked ... until find k stem.If there is the intersection of two or more k stem base-pair, then form false knot.

Definition: RNA subsequence S _i,jin, if (i, j), (i+1, j-1),, (k, l) is all base pair, i<k<l<j, then by (i, j) and (k, l) ∈ S the structure closed be called 1 stem, be expressed as S ₁[i, j].If 1 stem S ₁[i, j] by (i, j) and (r, s) ∈ S close, 1 stem S ₁[r ', s '] by (r ', s ') and (k, l) ∈ S close, i<r<r ' <k<l<s ' <s<j, v=r ’ – r+s-s ' >2, then by (i, j) and (k, l) ∈ S the structure closed be called 2 stems, be expressed as S ₂[i, j].

In like manner, if S ₁[i, j] by (i, j) with (r, s) ∈ S close, (k-1) stem by (r ', s ') and (k, l) ∈ S close, i<r<r ' <k<l<s ' <s<j, v=r ’ – r+s-s ' >2, then by (i, j) and (k, l) ∈ S the structure closed be called k stem, be expressed as S _k[i, j], S _kthe least energy of [i, j] is expressed as ES _k(i, j), k stem S _kthe length of [i, j] is expressed as LS _k(i, j)=k-i+1 or RS _k(i, j)=j-l+1.

If 2 stem S ₂[i, j] does not match base by two nested 1 stems and its inside and forms.If E ₂(r, r ': s ', s) represents the energy of base to 2 ring structures that (r, s) and (r ', s ') is formed, ES ₁(i, j) and ES ₁(r ', s ') represents by the energy of base to 1 stem that (i, j) and (r ', s ') closes respectively, then ES ₂(i, j)=ES ₁(i, j)+E ₂(r, r ': s ', s)+ES ₁(r ', s ').In like manner ES _k(i, j)=ES ₁(i, j)+E ₂(r, r ': s ', s)+ES _k-1(r ', s ').

If LS (i, j) ∈ is { LS ₁(i, j), LS ₂(i, j) }, ES (i, j) ∈ { ES ₁(i, j), ES ₂(i, j) }.In the method for the invention, the free energy of 1 stem and 2 stems and length use O (n ³) time pre-service and be stored in respectively in triangular matrix ES (i, j), LS (i, j), its computation process is shown in program 1.

In like manner, by ES _kthe computing formula of (i, j) is known, and the time complexity calculating k stem is O (n ³), space complexity is O (n ²).The calculating of k stem (k >=3) is realized by dynamic programming algorithm below.

K stem is made up of stem and 2 rings, and the energy sum of the heap superimposition ring of its free energy contained by it, any false knot can be analyzed to k stem and multi-branched ring.

Embodiment 1:

In the prediction of RNA pseudoknot structure, if in k stem during k=1 or k=2, the program computation of relevant 1 stem and 2 stems is as described below.

The energy of program 1:1 stem and 2 stems and the calculating of length

Fig. 4 provides a simple false knot.Use two 1 stem (S ₁[1,19], S ₁[7,30]) and three subsequence (s _6,6, s _13,14, s _20,24) form a false knot.Because each 1 stem is determined by two parameters, the storage of 1 stem needs O (n ²) space, the time complexity therefore calculating false knot is O (n ⁴), space complexity is O (n ²).

Known by Fig. 4: W (1,30)=ES ₁(1,19)+ES ₁(7,30)+W (6,6)+W (13,14)+W (20,24)

Embodiment 2:

A given sequence s=s ₁s ₂s _n, sequence fragment s _i,j=s _is _j, 1 < i < j < n.If W (i, j) is subsequence S _i,jthe corresponding least energy comprising the secondary structure S of false knot.If V (i, j) is s _iand s _jwhen forming base to (i, j), subsequence S _i,jthe corresponding least energy comprising the secondary structure S of false knot.

Fig. 5 provides the rated figure of W (i, j) and V (i, j).The W (i, j) comprising pseudoknot structure is calculated by following 4 kinds of situations:

1) s _jdo not match base, base s _iand s _j-1pair relationhip is not determined, as Fig. 5 .1, and W (i, the j)=W (i, j-1) of calculating;

2) s _ido not match base, base s _i+1and s _jpair relationhip is not determined, as Fig. 5 .2, and W (i, the j)=W (i+1, j) of calculating;

3) s _iand s _k, s _k+1and s _jdo not form base to and at different subsequence S _i,kand S _{k+1, j}in corresponding secondary structure, i<k<j, as Fig. 5 .3, calculating $W(i,j)=$ $\underset{i<k<j-1}{\min }(W(i,k)+W(k+1,j));$

4) s _iand s _jform base to (i, j), as Fig. 5 .4, W (i, the j)=min (V (i, j)) of calculating.

The V (i, j) comprising pseudoknot structure is calculated by following three kinds of situations:

(1) S is by base 1 ring closed to (i, j), as Fig. 5 .5, and V (i, the j)=minE of calculating ₁(i, j);

(2) S is by base 2 rings closed to (i, j) and (k, l), as Fig. 5 .6.

V(i,j)＝min(E ₂(i,k:l,j)+V(k,l)),i<k<l<j,u＝(k-i+j-l)-2<U

(3) S is k ring (k >=3) or pseudoknot structure, i<k<j, as Fig. 5 .6, calculating $V(i,j)=\min \underset{i<h<j-1}{\min }(W_M(i+1,h)+W_M(h+1,j-1)+M+P),$ Wherein M represents the penalty value of a formation multi-branched ring, and P represents the penalty value that in multi-branched ring, each base is right.W _midentical with the computing formula of W, but parameter is different, W _mbe specifically designed to the structure prediction of sequence fragment in multi-branched ring, and W is only for without the structure prediction of outer closures base to time series segment.

Method of the present invention compares with the experiment of PKNOTS algorithm

PknotsRG method only can predict the simple nested false knot be made up of two 1 stems, can not predict intersection false knot.Use C++ to realize method of the present invention, and compare with PKNOTS method.

Table 1 method of the present invention compared with the computing time of PKNOTS method

Computing time relatively in table 1.Method of the present invention is at double-core CPU:3.0GHz, and the PC inside saving as 4GB is tested, and PKNOTS algorithm high-performance computer Silicon Graphics Origin200 tests.As known from Table 1, computational length is the RNA sequence of 75 bases, and method of the present invention uses 51 seconds, and PKNOTS algorithm uses 20 minutes.Computational length is the RNA sequence of 105 bases, and method of the present invention uses 225 seconds, and PKNOTS algorithm uses 235 minutes.Computational length is the RNA sequence of 200 bases, and method of the present invention uses 72 minutes, and PKNOTS algorithm can not calculate.In fact, method of the present invention can success prediction length more than the secondary structure of the RNA sequence of 1500 bases.

Although the embodiment disclosed by the present invention is as above, the embodiment that described content just adopts for the ease of understanding the present invention, and be not used to limit the present invention.Technician in any the technical field of the invention; under the prerequisite not departing from the spirit and scope disclosed by the present invention; any amendment and change can be done what implement in form and in details; but scope of patent protection of the present invention, the scope that still must define with appending claims is as the criterion.

Claims (5)

1., based on a Forecasting Methodology for the RNA (ribonucleic acid) pseudoknot structure of k stem, it is characterized in that comprising the following steps:

Input one section of ribonucleic acid base sequence;

Definition false knot, k stem, (k >=1);

Search base and k stem from left to right, all k stems found out are marked;

Intersection according to two or more k stem base-pair forms pseudoknot structure characteristic, searches false knot;

Calculate the least energy of the RNA (ribonucleic acid) pseudoknot structure comprising k stem;

Export the pseudoknot structure of RNA (ribonucleic acid).

2. the Forecasting Methodology of the RNA (ribonucleic acid) pseudoknot structure based on k stem according to claim 1, is characterized in that: 1 stem (is designated as S ₁[i, j]) by base-pair (i, j) with (r, s) ∈ S close, if (k-1) stem by (r ', s ') and (k, l) ∈ S close, i<r<r ' <k<l<s ' <s<j, v=r ’ – r+s-s ' >2, then by (i, j) and (k, l) ∈ S the structure closed be called that k stem (is designated as S _k[i, j]).

3. the Forecasting Methodology of the RNA (ribonucleic acid) pseudoknot structure based on k stem according to claim 2, is characterized in that: the intersection of two or more k stem base-pair forms pseudoknot structure.

4. the Forecasting Methodology of the RNA (ribonucleic acid) pseudoknot structure based on k stem according to claim 1, is characterized in that: search base from left to right, according to 1 stem definition, first searches 1 stem, to all kilobase marker in 1 stem, searches k stem by that analogy and mark.

5. one kind comprises based on the prediction unit of the RNA (ribonucleic acid) pseudoknot structure of k stem:

Input block: it inputs one section of ribonucleic acid base sequence;

Definition unit: define 1 stem, 2 stems ... k stem;

Search unit: search base from left to right, to all 1 stems, 2 stems that find out ... base in k stem marks;

Pseudoknot structure searches unit: the intersection according to two or more k stem base-pair forms pseudoknot structure characteristic, searches false knot;

False knot computing unit: according to minimum free energy principle, calculates the least energy of the RNA (ribonucleic acid) pseudoknot structure comprising k stem;

Output unit: it is according to minimum free energy principle, exports the pseudoknot structure of ribonucleic acid base sequence.