摘要:
A homology retrieval can be performed with higher accuracy than conventional technologies when comparing a query sequence with a target sequence, and retrieving a similar location in the target sequence. The sequence information of a query sequence and a genomic-scale target sequence is acquired, the acquired information is compressingly converted into a compressed query sequence and a compressed target sequence in each of which a homopolymer region including two or more consecutive identical bases is replaced with a single base of the bases, the two sequences are compared, and a refining search is performed for a compressed target partial sequence that matches the compressed query sequence in the compressed target sequence. For the refined compressed candidate sequence and the query sequence, based on the information on the number of consecutive identical bases in the each of the sequences before compression, the number of consecutive bases is compared between the two compressed sequences for each corresponding base, and the degree of similarity indicating homology of the candidate sequence with the query sequence is computed from a degree of match or a degree of mismatch in the number of consecutive bases. By ranking and selecting an arbitrary number of candidate sequences having relatively high homology with the query sequence from this degree of similarity, it is possible to avoid the influence of the number of consecutive identical bases in a homopolymer region, thereby performing a homology retrieval accurately.
摘要:
A genetic motif extracting apparatus is adapted to extract a motif from genetic sequence information, where the motif has a regularity in a distinctive feature that specifies a genetic function. The genetic motif extracting apparatus includes a weight calculation unit for calculating a weight of each genetic sequence from a length of at least one branch of an evolution tree structure that is related to a plurality of genetic sequences, a score calculation unit for calculating a score that indicates a degree of similarity of sequence elements of the genetic sequences appearing at a site for each site of the genetic sequences using the weight calculated by the weight calculation unit, and a feature information extraction unit for extracting a part of the genetic sequence having the regularity in the distinctive feature as the motif based on the score calculated by the score calculation unit.
摘要:
The present invention relates to a method for modifying a property of a protein. The present invention also relates to a method for producing a protein which has a modified property, and a method for producing a microorganism which has a modified property. The present invention is useful in the field of microbial industrial production and the like.
摘要:
It is intended to identify or estimate miRNAs and one or more target genes (target mRNAs) targeted thereby.A method of predicting or identifying miRNAs and one or more target mRNAs targeted thereby, which comprises calculating the most stable secondary structures of double-stranded RNAs, which can be formed by all partial sequences in all of the subject mRNAs with miRNAs, and the secondary structure energies thereof to thereby search for all partial sequences capable of having stable structures through the binding of miRNAs to mRNAs, and then calculating the most stable secondary structure, which can be formed by a subject partial sequence or regions in the vicinity of the subject partial sequence with partial sequences of the concerned mRNA, and the secondary structure energy thereof to thereby determine whether or not the subject partial sequence of the concerned mRNA has a structure capable of interacting with the miRNA.
摘要:
A property of a protein is modified by the following steps: (a) selecting 1000 or more genes from the genome of a first microorganism, and selecting 1000 or more genes from the genome of a second microorganism, wherein the genes from the first microorganism are orthologs to the genes from the second microorganism, and wherein the second microorganism is closely related to the first microorganism, but grows differently under at least one optimum growth condition when compared with the first microorganism, (b) comparing an amino acid sequence encoded by a gene from the first microorganism to an amino acid sequence encoded by the orthologous gene from the second microorganism, (c) detecting substitutions between the amino acid sequence encoded by a gene from the first microorganism and the amino acid sequence encoded by a gene from the second microorganism for each pair of orthologous genes, (d) compiling the detected amino acid substitutions for each amino acid substitution type, (e) calculating the frequency of each amino acid substitution type, wherein for each detected amino acid substitution type, a correction is made by subtracting the total number of substitution types which occur from the first microorganism to the second microorganism from the total number of the same substitution type which occurs in the reverse direction, or from the second microorganism to the first microorganism, (f) identifying and labelling the amino acid substitutions which occur at a high frequency as amino acid substitutions which are involved in said optimum growth condition, and (g) introducing one or more of the amino acid substitutions identified in (f) into the gene encoding the protein to modify a property of the protein.
摘要:
A method for use in displaying an expression phenomenon in a living matter that are capable of displaying (printing), in a format directly appealing to the eyes or sense, information indicative of gene expression phenomena occurring with time to assist a researcher with easy elucidation of a gene network mechanism. It comprises memorizing means that memorizes an expression data in a cell unit or a site unit along a time axis; and processing means adapted to visualize and display a gene expression phenomenon on a display screen, and comprises the steps of displaying, as a three-dimensional image on a display screen, a shape of a living matter of a cell or site of which expression phenomenon is observed; setting a viewpoint on a three-dimensional space where the gene expression phenomenon in the shape of the living matter displayed is to be observed; and creating a three-dimensional image representing the expression phenomenon at the set viewpoint or at a fixed viewpoint, to display it in one color or multiple colors in various scales depending on a frequency of expression of a gene in the subject cell or site.
摘要:
It is intended to identify rheumatoid arthritis susceptibility genes by a highly efficient, low-cost mapping method using microsatellites. In the present invention, novel rheumatoid arthritis susceptibility genes, that is, TNXB, NOTCH4, RAB6A, MPRL48, UCP2, and UCP3 genes, in the human genomic DNA sequence were identified by conducting case-control association analysis on rheumatoid arthritis by use of microsatellite polymorphic markers assigned at approximately 100-kb intervals to narrow down candidate regions and then conducting association analysis and linkage analysis with SNP as a marker.