International Business Machines Corporation

Tetsuo Shibuya

Makoto Kano

Isidore Rigoutsos

Hisashi Kashima

Provided is a base sequence cluster generating system, method, and program product for performing cluster generation. The base sequence cluster generating system utilizes a computer system having a database containing base sequences receives a query sequence over. The computer uses spliced base sequences as a query sequence to generate a first cluster including base sequences that are likely to constitute a spliced pair with the query sequence. Spliced alignment is applied to the generated first cluster to generate a second cluster including spliced pairs. The generated second cluster is returned to the requester.

Base sequence cluster generating system, base sequence cluster generating method, program for performing cluster generating method, and computer readable recording medium on which program is recorded and system for providing base sequence information

Analyzes chromosomal states based on amounts of expression of genes. An example apparatus comprising: a unit for storing probability distribution of amounts of expression of genes for each chromosomal state, assuming any of the chromosomal states in which the distributions of amounts of expression are different; a unit for supplying state transition probability indicating probability in which when each of the genes arrayed on the chromosome assumes any one of the chromosomal states, a certain gene array assumes any one of the chromosomal states; an input unit for receiving an expression amount measurement value of the amount of expression for each of the genes on the chromosome; and a unit for detecting a combination of the chromosomal states maximizing a probability among those that can be assumed by the genes on the chromosome, based on the probability distribution and the state transition probability.

System and method for analyzing chromosomal states based on gene expression

The objective of the present invention is the efficient analyzation of the structure of an array. By performing the prev(S) calculation for a character string S, if in the character string S a like variable is present upstream of a second variable, the second variable is changed to a numerical value that indicates the distance to the upstream like variable. But if in the character string S a like variable is not present upstream of a variable, that variable is changed to '0' to obtain a character string S. Further, by performing the compl(S) calculation for the a character string S, if in the character string S a complementary variable is present upstream of a second variable, the second variable is changed to a numerical value that indicates the distance to the complementary variable. But if in the character string S a complementary variable is not present upstream of a variable, that variable is changed to '0' to obtain a character string S(). A single suffix tree (structure suffix tree) is generated by regarding the character strings Sand Sas a pair of corresponding character strings (to), and the obtained structure suffix tree is employed to analyze the structure of the array that is represented by the character string S.

Method for changing a target array, a method for analyzing a structure, and an apparatus, a storage medium and a transmission medium therefor

A base sequence cluster generating system, method, and program product for performing cluster generation is provided. This is accomplished utilizing a computer system having a database containing base sequences which receives a query sequence. The computer uses spliced base sequences as a query sequence to generate a first cluster including base sequences that are likely to constitute a spliced pair with the query sequence. Spliced alignment is applied to the generated first cluster to generate a second cluster including spliced pairs. The generated second cluster is returned to the requester.

A system for screening nucleotide sequences, a method therefor, a program, a recording medium, and a server on which the screening of nucleotide sequences is executed. The solution comprises a step of storing target nucleotide sequence data and a probe nucleotide sequence, a step of generating complementary sequence data from a probe nucleotide sequence that may be bound to the target nucleotide sequence, and storing a maximum acceptable edit distance between the target nucleotide sequence and the probe nucleotide sequence, a step of reading out each nucleotide sequence data and the maximum edit distance from each storing unit, and evaluating the binding possibility of the target nucleotide sequence data and the complementary sequence data in descending order of edit distance, and a step of storing the result of the binding evaluation in a storage unit.

Nucleotide sequence screening

A system and method for identifying genes that employs a pattern database, an input device for inputting a DNA sequence, and a processor for processing the DNA sequence and patterns to identify a putative gene. The processor may determine open reading frames (ORFs) in the DNA sequence, generate an amino acid translation for each ORF, and identify a match of a pattern in the amino acid translation.

System and method for identifying genes

The objective of the present invention is the efficient analyzation of the structure of an array. By performing the prev(S) calculation for a character string S, if in S, a like variable is present upstream of a second variable, the second variable is changed to a numerical value that indicates the distance to the upstream like variable. But if in S, a like variable is not present upstream of a variable, that variable is changed to '0' to obtain a character string S. Further, by performing the compl(S) calculation for S, if in the character string S a complementary variable is present upstream of a second variable, the second variable is changed to a numerical value that indicates the distance to the complementary variable. But if in S, a complementary variable is not present upstream of a variable, that variable is changed to '0' to obtain a character string S

A fast search is performed of a large text database, while suppressing an increase in the data size of the data structure used for the process. A pattern search method for searching a target character string for a desired pattern includes: a range search step and a character string extraction step. At the range search step, intermediate patterns are obtained by adding characters in order, one by one, from the last character of the pattern to the first, and a range is determined for a suffix array, which corresponds to the target character string, wherein the first character of each of the intermediate patterns is present. Then, at the character string extraction step, elements of the character string are designated that correspond to elements included in the range of the suffix array, and character string segments are extracted consisting of the same number of elements as the elements of the pattern and having the elements of the character string as their first characters.

Pattern search method, pattern search apparatus and computer program therefor, and storage medium thereof

A method is provided for allowing a database search that prevents an owner of the database or someone intercepting the database search in the network from knowing the contents of the query, without requiring any particular processing on the part of the database. Clientaccesses database serverwhich stores sequence patterns and inquires whether the sequence patterns stored in the database serverexist in a predetermined sequence. Clientcomprises sequence processing sectionfor dividing a search sequence subjected to search to create multiple subsequences; and query issuing sectionfor issuing a query to database serverusing the created multiple subsequences individually as a query sequence.

Database search device, database search system, database search method, program and storage medium

An efficient method and system is provided for searching for the shortest paths between a source and multiple destinations, and between multiple sources and multiple destinations. The speed of the conventional Dijkstra method, which is the basic calculation method, is increased by employing information concerning the relationship between a node and a set of destinations on a graph. The relationship information is constituted by the estimate function h(v) concerning a specific node v and a set T of destinations, where h(v) is a lower bound of all the shortest path lengths extending from node v to each of the destination sets T. Employment of the estimate function can increase the speed of the Dijkstra method.

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Yamato, Japan

Tetsuo Shibuya