Method and apparatus for manifesting characteristic existing in symbolic sequence

Abstract: A method which manifests characteristic which is latent and can not be recognized, although it exists in a complicated symbolic sequence, for example, a nucleotide sequence of DNA, and thereby enables recognition of the characteristic unrecognized yet, is provided. When a symbolic sequence I j (j = 1∼m) is given, there is an effected conversion to a parallel sequence A(k) of partial symbolic sequences in which the suffix j is aligned in the following positional relation: and A(k) is formed with changing k to p, p+r, p+2r, p+3r ... , and the whole parallel sequences ΣA(k) is obtained. When regularity of period length k exists in the symbolic sequence I j , the regularity remarkably appears in the partial symbolic sequences obtained by extracting one symbol at every k-1 symbols from the symbolic sequence.

Description: BACKGROUND OF THE INVENTION Field of the Invention The present invention relates to a method and apparatus for manifesting characteristic or regularity which is latent and can not be recognized, although such characteristic or regularity actually exists in a complicated symbolic sequence, for example, a nucleotide sequence of DNA or an amino acid sequence of protein. In these sequences, regularity can not be recognized at a glance even when the regularity is included. The present invention enables recognition of characteristic or regularity included in the symbolic sequence but unrecognized yet. Description of the Related Art Some complicated symbolic sequences contain characteristic which has not been recognized by human beings, although the characteristic actually exists. For example, genetic information is specified by a symbolic sequence of long string. The symbols consist of four symbols each indicating one of four kinds of nucleotides. A large amount of symbols are one-dimensionally aligned. In the study of genetic information, it is extremely important to recognize a certain regularity hidden in the symbolic sequence indicating genetic information. For such a purpose, various trials have been made for analyzing a symbolic sequence based on a variety of mathematical methods such as the Fourier analysis. However, these trials have not necessarily accomplished successful results. One problem with the conventional analysis methods is that even if a certain regularity is included in a part of a very long symbolic sequence, the regularity existing partially is buried in the whole sequence and can not be recognized when the whole symbolic sequence is analyzed. Since there is no effective technology to know in advance in which part of the sequence the regularity exists, there are many characteristics or regularity which can not be recognized by the conventional analysis methods. Equidistant Letter Sequences in the Book of Genesis (Doron Witztum, Eliyahu Rips and Yoav Rosenberg, Statistical Science 1994, Vol. 9, No. 3, page 429-438) introduces a technology in which a code hidden in a one-dimensional letter sequence is decoded by converting the one-dimensional letter sequence to a parallel sequences A(k) of partial symbolic sequences. In this technology, there is required as operation to extract letters having senses from the parallel sequence A(k) of partial symbolic sequences, and it can not be used for other sequences than the letter sequence. Further, when a certain regularity is to be recognized in a symbolic sequence which is irregular at a glance and which is often found in a natural field, inconsistency, namely, regularity can not be recognized unless the regularity to be recognized has been recognized in advance, can not be solved. SUMMARY OF THE INVENTION An object of the present invention is to contrive a method and apparatus which manifests characteristic or regularity in a symbolic sequence representing DNA, RNA or protein, even if such characteristic or regularity exists only in a part of the whole symbolic sequence, and thereby enables recognition of characteristic or regularity which has not been recognized until now. This object is achieved by a method according to claim 1 and an apparatus according to claim 6, respectively. Further developments of the invention are given in the dependent claims. The present invention allows to manifest characteristic or regularity existing throughout the entire sequence. In the present invention described above, since a parallel sequence (matrix) A(k) of partial symbolic sequences can be output using one or more expression means selected from hue, lightness and saturation of color, even if regularity is not known in advance, that regularity can be manifested by a pattern of hue, lightness and saturation of color and can be easily recognized. Here, n represents an integer such that nk<m ≦nk+k, and when the suffix j is m+1 or more, the processing is ignored. In this case, a parallel sequence made by parallel-positioning of p partial symbolic sequences matrices, a parallel sequence made by parallel-positioning of p+r partial symbolic sequences, and parallel sequences made by parallel-positioning of likewise increased number of partial symbolic sequences, are all parallel-positioned. In this processing, if regularity of period length αis hidden in the symbolic sequence, such regularity is remarkably manifested in a parallel sequence A( α ) made by parallel-positioning of partial symbolic sequences of a number of α. If α is included in between p, p+r, p+2r, p+3r, ··· ··· ··· rows, regularity of period length α is manifested in a parallel sequence of partial symbolic sequences of an analogous number to α. Therefore, increment r regarding the number of the partial symbolic sequences is not necessarily required to be one, and it may advantageously be any natural number. In this case, when the increment r is smaller, characteristic is more securely manifested. In this embodiment, regularity of an unknown period length is manifested in a parallel sequence of partial symbolic sequences of some number, and recognition of characteristic becomes easy. In the above-described method, it is preferable that each symbol is expressed by combination of hue, lightness and saturation of color. By this embodiment, as a result of the manifestation of characteristic hidden in the symbolic sequence through visual sense, there will be made more sufficient understanding regarding characteristic hidden in the symbolic sequence, and various applications and developments utilizing the characteristic are made possible. Further, the resulting visual pattern is a pattern including regularity and irregularity mixed which has not conventionally existed, and a visual pattern of which design itself has utility application can be designed. When one symbol is taken out from an original symbolic sequence at an interval of k-1 (namely, at every k) to make a symbolic sequence and the method is applied to this extracted symbolic sequence, if regularity of period length k is hidden in the original symbolic sequence, the regularity is manifested and appears remarkably. When one symbol is taken out from an original symbolic sequence at an interval of kq-1 (namely, at every kq) to make a symbolic sequence and the method is applied to this extracted symbolic sequence, if regularity of period length kq is hidden in the original symbolic sequence, the regularity is manifested and appears remarkably. Any of the above-described methods are conducted with changing k to p, p+r, p+2r ··· ··· ··· , and there are formed whole parallel sequences ∑ A(k) of a parallel sequence A(p) made by parallel-positioning of p partial symbolic sequences, a parallel sequence A(p+r) made by parallel-positioning of p+r partial symbolic sequences, and parallel sequences made by parallel-positioning of likewise increased number of partial symbolic sequences, and regularity of period length α appears remarkably in a parallel sequence A( α) formed by parallel-positioning of k (=α) partial symbolic sequences. Therefore, characteristic or regularity of unknown period length is manifested, and recognition of characteristic or regularity becomes easy. According to this method, even if the period length α of regularity or characteristic is included between p, p+r, p+2r, ··· ··· ··· rows, characteristic or regularity is manifested in a parallel sequence formed by parallel-positioning partial sequences of a number approximated to α, and increment r is not necessarily required to be one. It becomes possible to manifest characteristic by small amounts of data processing, by selecting increment r adjusted to events. Further, by outputting analyzed results by color, expressions suitable to event and observer become possible, and characteristic is more easily recognizable. The resulted color pattern will be an interesting pattern in which regularity and irregularity are mixed, and the method can be utilized also as a designing method. Especially when an initiation position of regularity is situated at an analysis initiation position, the pattern of having a parabolic shape clearly appears, and regularity of a long period length is manifested clearly, in the whole parallel sequences ∑A(k). The present invention will be recognized more successfully by reading the descriptions of the following examples with the referring drawings. BRIEF EXPLANATION OF THE DRAWINGS Fig. 1 represents the whole parallel sequences Σ A(k) formed from a nucleotide sequence of human genomic DNA. Fig. 2 represents positional relation of suffix j in Fig. 1. Fig. 3 represents the whole parallel sequences ΣA(k) formed from a numerical sequence showing π. Fig. 4 represents the whole parallel sequences ΣA(k) formed from a circulating numerical sequence of period length 18 (symbolic sequence). Fig. 5 represents the whole parallel sequences ΣA(k) formed from a circulating numerical sequence of period length 12 (symbolic sequence). Fig. 6 represents a part of the whole parallel sequences ΣA(k) formed from an amino acid sequence of muscle protein myosin. Fig. 7 represents another part of the whole parallel sequences ΣA(k) formed from the amino acid sequence of muscle protein myosin. Fig. 8 represents still another part of the whole parallel sequences ΣA(k) formed from the amino acid sequence of muscle protein myosin. Fig. 9 represents existing positions of vowel 'O' appearing in 'Genji Monogatari'. Fig. 10 represents placing positions in converting 100 symbolic sequence into the whole parallel sequences ΣA(k). Fig. 11 explains pre-treatments for symbolic sequences. Fig. 12 represents another example of placing positions in converting a symbolic sequence into the whole parallel sequences ΣA(k). Fig. 13 represents the whole parallel sequences ΣA(k) formed from cDNA sequence of a G protein β subunit. Fig. 14 represents extraction of symbolic sequence I to be processed with changing the initial point, from a symbolic sequence M. Fig. 15 represents an example in which parabolic pattern appears in the whole parallel sequences ΣA(k) formed from a genomic DNA sequence of baker's yeast. Fig. 16 represents constitution of an apparatus for effecting the method of the present invention. DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS Experimental examples embodying the present invention will be introduced below. [First experimental example] Fig. 1 represents an experimental example for processing a symbolic sequence I j showing nucleotide sequence of human genomic DNA. A symbolic sequence I j indicating nucleotide sequence of human genomic DNA is formed by one-dimensional sequence of an enormous amount of symbols, each symbol indicating one of four kinds of nucleotides ATGC, and a certain regularity hidden therein is recognized as useful information. Therefore, it is a large object in genetic study to find regularity, or to specify a part of the sequence including the regularity. Fig. 1 represents a processed result output through color, and four kinds of symbols ATGC are, respectively, expressed by four colors red, blue, green and yellow. The original image of Fig. 1 is expressed in four colors. Fig. 1 represents a result when the present invention is conducted with p=5 and r=1. Referring to an example of a parallel sequence A(17) in which k=17, as shown in Fig. 2, longitudinal partial symbolic sequences C1, C2, C3 ··· ··· C17 which are extracted from a symbolic sequence I j at every k and aligned longitudinally, are laterally aligned to form a parallel sequence A(17). In C1, C2, C3 ··· ··· , values of suffixes j of symbols to be extracted are shifted by one. This rule is common to all k values and to all partial symbolic sequences C. In this example, a symbol group extracted at every k is placed longitudinally to form a longitudinal partial symbolic sequence, and the longitudinal partial symbolic sequences are laterally placed. However, longitudinal to lateral relations may be reversed, and a symbol group extracted at every k may be placed laterally to form a lateral partial symbolic sequence, and the lateral partial symbolic sequences may be longitudinally placed. In Fig. 1, B16 remarkably shows that a repeating pattern of period length 16 exists in a part of the nucleotide sequence. From the pattern B16, it is possible to learn that there is a possibility that useful information is included in this part, and this part is a area valuable to be analyzed in detail. B17 and B16 represent the same regularity. The regularity of period length 16 appears as the vertical stripes in B16, and appears as the inclined stripes in B17. The inclined stripes in B17 has a pattern in which the left side is lowered. B18 also represents the same regularity, and the inclination of the stripes in B18 is closer to horizontal than in B17. The same regularity is also shown in a parallel sequence A(19) in which k=19, however, in this case, the inclination is almost horizontal, and extraction of characteristic becomes increasingly difficult. Regularity of period length α appears vertically and is expressed most remarkably in A( α) in which k (=α) partial symbolic sequences are parallel-positioned. However, the regularity also appears in a parallel sequence of partial symbolic sequences in which k= α+1 and k= α+2. Therefore, it is confirmed that the increment r is not necessarily required to be 1. A18 shows regularity of period length 18, and the same regularity is shown as pattern A17 in which the right side is lowered in the parallel sequence A(17) in which k=17, and shown as pattern A19 in which the left side is lowered in the parallel sequence A(19) in which k=19. In addition, many remarkable patterns appear in Fig. 1, and characteristics hidden in a nucleotide sequence of human genomic DNA are grasped from these patterns. Initial number p in the whole parallel sequences of partial symbolic sequences may be any natural number, and in Fig. 1, p=5. The increment r is not limited to 1, and it may be 2 or more. When r is smaller, characteristics are never failed to be found, and when r is larger, the amount of data processing is smaller. The increment r is not required to be constant, and it is preferable to select the increment r according to events. Fig. 16 represents an apparatus for effecting the above-described processing method, and in this apparatus, a symbolic sequence I j to be analyzed is memorized in a memory apparatus 181, and an apparatus 182 converts the symbolic sequence Ij into a parallel sequence A(k), and apparatus 183 forms the whole parallel sequences ΣA(k) in which a plurality of parallel sequences A(k) obtained by changing the value of k are parallel-positioned, and an apparatus 184 outputs the whole parallel sequences Σ A(k). The apparatus 182 and the apparatus 183 may be constituted of a computer and the apparatus 184 may be constituted of a color printer. It is preferable that Fig. 1 is expressed with a time lapse according to speed for processing the symbolic sequence. For example in Fig. 1, color corresponding to I1 is first expressed on the left upper summits of A(5) to A(21), and further expressions of I2, I3, I4 ··· ··· are effected in succession. By using this change in time, characteristics are more easily recognized, and also in the case of output by sound, output with time lapse is effective, and when output with time lapse is conducted, characteristics are recognized through changes in sound. Fig. 3 exemplifies a result obtained by processing π symbolic sequence (numerical sequence), and 10 kinds of symbols (number) 0 to 9 are expressed by 10 equally divided colors of spectrum from a violet to red. It is found from the expression result of Fig. 3 that specific symbols (numbers) tend to appear frequently in a specific range. When noise input is processed as a row of a symbolic sequence and this symbolic sequence is processed to obtain similar pattern as in Fig. 3, it becomes possible to extract characteristic existing in the noise and to extract only meaningful sound included in the noise. Further, it is known that the pattern shown in Fig 3 can be used, for example, as a ground pattern for securities, and this complicated ground pattern can be specified by a one-dimensional symbolic sequence. Fig. 4 represents a result obtained by processing a circulating numerical sequence of period length 18, and various patterns can be drawn according to the number k of a partial symbolic sequences to be fractionated. Various textile patterns can be designed by this pattern creating technology. Fig. 5 represents a processed result of a circulating numerical sequence of period length 12, and it is confirmed that different patterns from those of Fig. 4 can be made. According to this method, the complicated pattern shown in Fig. 3 and the regular patterns shown in Figs. 4 and 5 can be designed by the same method. Further, various patterns having utterly different impressions can be produced by changing corresponding relations of a symbol to a color. Figs. 6 through 8 represent a result obtained by processing a symbolic sequence which shows an amino acid sequence of a protein myosin of an adductor muscle of a scallop. In Figs. 6 to 8, basic residue is shown in blue, polar residue is shown in green, acidic residue is shown in red, and hydrophobic residue is shown in yellow. In Fig. 6, a remarkable yellow longitudinal stripe appears in a parallel sequence in which k=7, and the existence of regularity of ng a period length 7 is found. This regularity of a hydrophobic residue of period length 7 corresponds to α-helix, and by this method, the existence of α-helix can be recognized and the existing position thereof can be specified. This α-helix is manifested as yellow longitudinal stripes in parallel sequences in which k=7, 14, 28 and 35, and manifested as yellow diagonal lines in parallel sequences in which, for example, k=22, 27 and 29. Fig. 9 represents an example expressing dots in positions where vowel 'O' appears, prepared by applying the present invention to a symbolic sequence showing a row of vowels in Genji Monogatari. The left side represents an analysis result of the Kiritsubo chapter, and the right side represents an analysis result of the Hahakigi chapter. There is manifested characteristic that appear with frequency in vowel 'O' as high in the specific range of the document, and as low in other specific ranges. By this method, extraction of characteristic in a letter information becomes easy. Fig. 10 schematically represents processing contents for a symbolic sequence I j (j=1 to 100) to be processed. When, the period length of regularity to be extracted is known in advance, it will be easily recognized whether the regularity of the known period length k really exists, and in the case of existence, where it exists, by forming a parallel sequence A(k) in which partial symbolic sequences obtained by division into k fractions are parallel-positioned. Even when the period length is not known, regularity of the unknown period length is manifested at some location in the whole parallel sequences. Fig. 11 represents an example of pre-processing for a symbolic sequence to be processed, and when part of a symbolic sequence J shown in (A) is processed, the part to be processed as shown in (B) will be the whole symbolic sequence I of the present invention. Further, when one symbol is specified by combination of a plurality of symbols, this method is applied for the symbolic sequence specified by combination of a plurality of symbols, for example, as shown in (C). Alternatively, it may also be permissible that one symbol is obtained from symbols of order 123 in a symbolic sequence K, then, one symbol is obtained from symbols of order 234 in a symbolic sequence K, this procedure is repeated to effect conversion into one symbolic sequence I, and this converted symbol I is processed by the method, as in the case for calculating moving average. Further, as shown in (E), for a symbolic sequence existing in a symbolic sequence at specific period, it may also be permissible that a symbolic sequence of this period is first extracted, and the present invention is applied to the extracted symbolic sequence. Instead of this method, processing as exemplified in Fig. 12 may be effected. In this method, one symbol is extracted at every kq, for a partial symbolic sequence of longitudinal direction. In the case shown in this drawing, the result is obtained by effecting the method with changing k to 2, 3, 4 ··· and q is fixed at 5. The result corresponds to the result when a symbol of an order of 5 · 10 · 15 ··· is first extracted, and then the extracted sequence is separated into k partial symbolic sequences, and the resulted partial sequences are parallel-positioned to obtain a parallel sequence. By this method, it is possible to manifest regularity further hidden in a symbolic sequence hidden in a symbolic sequence L (shown in (E) of Fig. 11). When a parallel sequence of partial symbolic sequences are obtained as described above, various method can be adopted for expressing the result, and a method in which a symbol is expressed by color, a method in which a symbol is expressed by variation in color density and a method in which a symbol is expressed by a character (two dimensional pattern) may be adopted. The present invention is useful for analyzing various symbolic sequences, and useful in analyzing a nucleotide sequence of DNA, a nucleotide sequence of RNA, an amino acid sequence of protein, a numerical sequence, a letter sequence, a sound sequence and the like. By this analysis, it becomes possible to specify an existing position of useful information and to extract useful information. Further, when this method is applied to two symbolic sequences which can not be distinguished at a glance, characteristics are manifested, and the identity can be easily judged. In this sense, characteristics and regularity manifested in this method are not restricted to a repeating pattern having a certain period, and characteristics found in distribution of appearing sequence are also manifested. Further, the increment r in the number of partial symbolic sequences is not necessarily required to be 1, and further, it may not be a constant number. By effecting this method according to k1, k2, k3 ··· distributing irregularly, characteristics existing in two or more symbolic sequences are manifested, and the identity is easily judged. Fig. 13 represents the analysis result of a cDNA sequence of a G protein β subunit, and represents the result when the whole parallel sequences ΣA(k) is obtained when p is 5. In the original image of Fig.13, GCTA are expressed by 4 colors and three apparent different color zones are recognized. The boundary 101 of the color zones corresponds approximately to the position of j=281, and the boundary 102 of the color zones corresponds approximately to the position of j=1303. In this case, it is known that a coding range exists in the range from j=281 to j=1303, and it is recognized that the coding range is easily specified through visual sense in this method. Fig. 14 represents a procedure to obtain symbolic sequence I to be processed when changing the initial point, from a one-dimensional symbolic sequence M. For example, symbolic sequence I6 to be processed is a symbolic sequence obtained by extraction of M(6) and the following. When the present invention is performed on symbolic sequences I1, I2, I3, I4 ··· thus extracted to obtain the whole parallel sequences ΣA(k), a clear pattern may be obtained in the whole parallel sequences ΣA(k) corresponding to specific I. Fig. 15 represents one example thereof, and in the original image which is expressed in multicolor, a plurality of parabolic lines 151, 152, 153 ··· appear. As a result of intensive study of this phenomenon, it has been recognized that the above-described line group appears when the initiation point of regularity coincides with the initiation point of the symbolic sequence to be processed. By this, it has been known that the initiation point of regularity can be specified by utilizing appearance of a line group. Further, it is also known that the appearance gap of a group of lines 151, 152, 153 ··· and other group of lines 161, 162, 163 ··· corresponds to regularity of an extremely long period, and it has also been recognized that the regularity of an extremely long period can be recognized by utilizing a line group. The above-described explanations are only some specific examples. The scope of the claimed invention is defined by the attached claims.

Claims: A method of visualizing a regularity hidden in a sequence of symbols I j representing DNA, RNA or protein, the suffix j=1,2,..,m, which symbols are selected from specific symbols, the method being implemented on an apparatus, the method comprising a step of effecting a conversion of the symbolic sequence I j representing DNA, RNA or protein into a plurality of matrices, each matrix being of the type of a matrix A(k) having (n+1) lines and k columns, wherein the matrix elements are in the following positional relation; the plurality of matrices being composed of A(p), A(p+r), A(p+2r), A(p+3r),...., wherein p is a natural number with 2 ≦ p ≦ (m- 1 ), r is a natural number and n<m/k≦n+1, a step of expressing each of the specific symbols by a different color, and a step of outputting the plurality of matrices, in which the specific symbols are displayed by the different colors and the plurality of matrices are positioned in parallel. The method of claim 1, wherein the regularity is unknown. The method according to claim 1 or 2, further comprising a step of making the symbolic sequence I j by taking out the m symbols sequentially at every q from a symbolic sequence Ls, s=1 to t and t>mq. A data processing apparatus adapted to conduct a method according to one of claims 1 to 3.

Inventors: OBATA NOBUAKI, OOSAWA KENJI, YOSHIDA TETSUHIKO, OBATA, NOBUAKI, OOSAWA, KENJI, YOSHIDA, TETSUHIKO
Applicants: TOA GOSEI KABUSHIKI KAISHA
Application year: 1998
Main classification: G06F17
IPC codes: G06F19, G06F17, G06T7, G06T1