公开(公告)号：JP2007257017A

公开(公告)日：2007-10-04

申请号：JP2006076890

申请日：2006-03-20

Applicant: Biomatics Inc ,  株式会社バイオマティクス

Inventor： ARAKAWA HIROKI ,  NAMIMA KATSUYA ,  ISHIDA KANAKO ,  TADA MITSUHIRO

IPC: C12N15/09 ,  G06F19/00 ,  G06F19/16 ,  G06F19/22

Abstract: PROBLEM TO BE SOLVED: To accurately retrieve biological sequence information, at high speed, having an important secondary structure, such as a functional RNA, from a retrieval target database which stores a large quantity of biological sequence information. SOLUTION: The retrieval device of biological sequence information 100 comprises: a central processing part 200: and a parallel processing part 300 arranged in an element different from the central processing part 200, and is configured to communicate with the retrieval target database 102 related to the biological sequence information. The parallel processing part 300 includes a first candidate sequence extraction part 302 for extracting a first candidate sequence in which a value obtained by a first inquiry function satisfies a predetermined criterion. The central processing part 200 includes a second candidate sequence extraction part 214 for extracting a second candidate sequence in which a value obtained by a second inquiry function satisfies the predetermined criterion. In addition, the first inquiry function and the second inquiry function are functions for calculating structural validity when the biological sequence information is applied to inquiry structure patterns. COPYRIGHT: (C)2008,JPO&INPIT

Abstract translation: 要解决的问题：从存储大量生物序列信息的检索目标数据库中以高速准确地检索具有重要二级结构（例如功能性RNA）的生物序列信息。 解决方案：生物序列信息100的检索装置包括：中央处理部分200和并行处理部分300，其布置在与中央处理部分200不同的元素中，并且被配置为与检索对象数据库102通信 与生物序列信息有关。 并行处理部300包括：第一候选序列提取部302，用于提取通过第一查询函数获得的值满足预定标准的第一候选序列。 中央处理部200包括用于提取第二候选序列的第二候选序列提取部214，其中由第二查询函数获得的值满足预定标准。 此外，第一查询功能和第二查询功能是当将生物序列信息应用于查询结构模式时计算结构有效性的函数。 版权所有（C）2008，JPO＆INPIT

公开(公告)号：JP2007257020A

公开(公告)日：2007-10-04

申请号：JP2006076913

申请日：2006-03-20

Applicant: Biomatics Inc ,  株式会社バイオマティクス

Inventor： ARAKAWA HIROKI ,  NAMIMA KATSUYA ,  ISHIDA KANAKO ,  TADA MITSUHIRO

IPC: C12N15/09 ,  G06F19/00 ,  G06F19/22

Abstract: PROBLEM TO BE SOLVED: To accurately retrieve target biological sequence information at high speed from a retrieval target database which stores a large quantity of biological sequence information. SOLUTION: The retrieval device of biological sequence information 100 comprises: a central processing part 200: and a parallel processing part 300 arranged in an element different from the central processing part 200, and is configured to communicate with the retrieval target database 102 related to the biological sequence information. The central processing part 200 includes a parallel processing inquiry sequence generation part 204 for generating a parallel processing inquiry sequence based on an inquiry sequence. The parallel processing part 300 includes a first candidate sequence extraction part 302 for performing sequence matching between the parallel processing inquiry sequence and the retrieval target database 102, and for extracting a first candidate sequence. The central processing part 200 further includes a second candidate sequence extraction part 210 for performing the sequence matching between the inquiry sequence and the first candidate sequence, and for extracting a second candidate sequence. COPYRIGHT: (C)2008,JPO&INPIT

Abstract translation: 要解决的问题：从存储大量生物序列信息的检索目标数据库中高速准确地检索目标生物序列信息。 解决方案：生物序列信息100的检索装置包括：中央处理部分200和并行处理部分300，其布置在与中央处理部分200不同的元素中，并且被配置为与检索对象数据库102通信 与生物序列信息有关。 中央处理部200包括并行处理查询序列生成部204，用于基于查询序列生成并行处理查询序列。 并行处理部分300包括用于执行并行处理查询序列与检索目标数据库102之间的序列匹配并用于提取第一候选序列的第一候选序列提取部分302。 中央处理部分200还包括用于执行查询序列与第一候选序列之间的序列匹配并用于提取第二候选序列的第二候选序列提取部分210。 版权所有（C）2008，JPO＆INPIT

公开(公告)号：JP2004234297A

公开(公告)日：2004-08-19

申请号：JP2003021576

申请日：2003-01-30

Applicant: Biomatics Inc ,  株式会社バイオマティクス

Inventor： TADA MITSUHIRO ,  ASADA KAZUNORI ,  ARAKAWA HIROKI ,  KAWAI KEN ,  KAMISAKA MIKA ,  KOBAYASHI MASAKO

IPC: G01N33/48 ,  C12N15/09 ,  G06F17/30

Abstract: PROBLEM TO BE SOLVED: To speed up processing of analysis on biological sequence information such as a base sequence and an amino acid sequence. SOLUTION: A comparator 28 compares sequence information with a reference sequence by parallel collation processing. A sequence processing control part 30 controls the comparator 28, feeds the reference sequence to the comparator 28, and obtains a comparison result from the comparator 28. When the sequence processing control part 30 makes the comparator 28 operate parallel collation processing, in which a wild card is set at a site equivalent to a part of the reference sequence, a processing result of the sequence information is obtained. The sequence processing control part 30 offers the reference sequence with a wild card set in a part to the comparator. Using the reference sequence in which the wild card is set, similarity search is carried out. An amino acid sequence code area is retrieved by using the reference sequence in which the wild card is set to the site, in which bases corresponding to kinds of the amino acid are unspecified, is used. COPYRIGHT: (C)2004,JPO&NCIPI

公开(公告)号：JP2004234296A

公开(公告)日：2004-08-19

申请号：JP2003021561

申请日：2003-01-30

Applicant: Biomatics Inc ,  株式会社バイオマティクス

Inventor： TADA MITSUHIRO ,  ASADA KAZUNORI ,  ARAKAWA HIROKI ,  KAWAI KEN ,  KAMISAKA MIKA ,  KOBAYASHI MASAKO

IPC: G01N33/48 ,  C12N15/09 ,  G06F17/30

Abstract: PROBLEM TO BE SOLVED: To speed up processing of analysis on biological sequence information such as a base sequence and an amino acid sequence. SOLUTION: A comparator 28 compares sequence information with a reference sequence by parallel collation processing. A sequence processing control part 30 controls the comparator 28, feeds a sequence processing control reference sequence to the comparator 28, and obtains a comparison result from the comparator 28. The sequence processing control part 30 includes a mask processing part 46 turning at least a part of the sequence information written in the comparator 28 into a masked condition in which sequence elements are not distinguished. When mask processing by the mask processing part 46 based on the comparison result by the comparator 28 is carried out, a processing result of the sequence information is acquired. COPYRIGHT: (C)2004,JPO&NCIPI

公开(公告)号：JP2005251192A

公开(公告)日：2005-09-15

申请号：JP2005043118

申请日：2005-02-18

Applicant: Biomatics Inc ,  株式会社バイオマティクス

Inventor： ARAKAWA HIROKI ,  TAKAGI KOSUKE

IPC: C12N15/00 ,  G06F17/30 ,  G06F19/00 ,  G06F19/22 ,  G06F19/28

Abstract: PROBLEM TO BE SOLVED: To accelerate analysis processing of biological sequence information such as a base sequence and an amino acid sequence. SOLUTION: A storage processor having a parallel collation function, typically a CAM, namely Content Addressable Memory is used. Sequence information is stored in the storage processor to be used as collated data. Sequence analysis information is obtained by making the storage processor collate the collating data with the collated data by parallel processing and obtaining information indicating coincidence between the collating data and the collated data. In a preferable embodiment, a plurality of sequences are stored in the CAM which is the storage processor so that they are arranged in the collating direction by turning the direction to cross the collating direction. The same character string is used as the collating data. Whether or not the plurality of sequences coincide is determined by collation of the CAM. When the plurality of sequences are excluded from collating objects one by one, what sequence is different is understood. COPYRIGHT: (C)2005,JPO&NCIPI

Abstract translation: 待解决的问题：加速生物序列信息如碱基序列和氨基酸序列的分析处理。 解决方案：使用具有并行核对功能的存储处理器，通常为CAM，即内容可寻址存储器。 序列信息存储在存储处理器中以用作对照数据。 通过使存储处理器通过并行处理将对照数据与对照数据进行比较，并获得指示对照数据和对照数据之间的一致性的信息，获得序列分析信息。 在优选实施例中，多个序列存储在作为存储处理器的CAM中，使得它们通过转动方向来交叉整理方向而布置在对照方向上。 使用相同的字符串作为整理数据。 多个序列一致是否通过CAM的核对确定。 当将多个序列逐一排除对齐时，可以理解什么序列是不同的。 版权所有（C）2005，JPO＆NCIPI

公开(公告)号：JP2005216320A

公开(公告)日：2005-08-11

申请号：JP2005043127

申请日：2005-02-18

Applicant: Biomatics Inc ,  株式会社バイオマティクス

Inventor： ARAKAWA HIROKI ,  TAKAGI KOSUKE

IPC: C12N15/00 ,  G06F17/30 ,  G06F19/00 ,  G06F19/22 ,  G06F19/28

Abstract: PROBLEM TO BE SOLVED: To speed up the analysis of biological sequence information such as base sequences and amino acid sequences. SOLUTION: A storage processing apparatus with a parallel collating function, typically a CAM (Content Addressable Memory) is used. Sequence information is stored in the storage processing apparatus for use as data to be collated. Collating data and the data to be collated are collated through parallel processing by the storage processing apparatus to obtain information showing the coincidence of the collating data with the data to be collated to thereby obtain sequence analysis information. In a preferred embodiment, a plurality of sequences are stored in the CAM as the storage processing apparatus while being pointed in a direction perpendicular to the direction of collation and aligned in the direction of collation. The same letter string is used as the collating data. Through collation by the CAM, a determination is made as to whether or not the plurality of sequences are coincident with one another. By excluding the plurality of sequences one by one from the subject of collation, one can see which of the sequences are different. COPYRIGHT: (C)2005,JPO&NCIPI

Abstract translation: 要解决的问题：加快​​生物序列信息的分析，如碱基序列和氨基酸序列。 解决方案：使用具有并行对照功能的存储处理装置，通常为CAM（内容可寻址存储器）。 序列信息存储在存储处理装置中，用作待整理的数据。 整理数据和要整理的数据通过存储处理装置的并行处理进行整理，以获得表示对照数据与要整理的数据一致的信息，从而获得序列分析信息。 在优选实施例中，多个序列作为存储处理设备存储在CAM中，同时指向与校准方向垂直的方向并且在排序方向上对齐。 使用相同的字母串作为整理数据。 通过CAM的对照，确定多个序列是否彼此一致。 通过从对照对象中逐个排除多个序列，可以看出哪个序列是不同的。 版权所有（C）2005，JPO＆NCIPI

公开(公告)号：AU2002366918A1

公开(公告)日：2003-07-09

申请号：AU2002366918

申请日：2002-12-11

Applicant: BIOMATICS INC

Inventor： ARAKAWA HIROKI ,  TAKAGI KOSUKE

IPC: C12N15/09 ,  G06F17/30 ,  G06F19/00 ,  G06F19/22

Abstract: Storage processor having a parallel matching function, typically, a CAM or content addressable memory. Sequence information is stored in a storage processor to use it as to-be-matched data. Matching data and the to-be-matched data are matched parallel by the storage processor. Information representing the matching between the matching data and the to-be-matched data is obtained, and thereby sequence analysis information is obtained. In a preferred mode, sequences are so stored in a CAM serving as the storage processor as to be directed perpendicularly to the matching direction and arranged in the matching direction. The matching data used is a same-character string. From the matching by the CAM, it is judged whether or not the sequences match one another. When sequences are excluded from the matching object one by one, which sequence is different is found. Analysis of biological sequence information such as on a base sequence and amino acid sequence is conducted in a shorter time.

公开(公告)号：EP0154557A2

公开(公告)日：1985-09-11

申请号：EP85301579.0

申请日：1985-03-07

Applicant: Biomatics Inc.

Inventor： Gardos, Ivan

IPC: G01N1/28

CPC classification number: G01N1/31 ,  B05C3/05 ,  B05C13/02

Abstract: A magnetic lifting device for lifting a stack of specimen holders out of one tube and lowering them into another tube is disclosed. The device avoids the necessity of manual handling of the stack. ln the device there are a number of stack holding tubes, each one open at the top, positioned in a circle about a vertical axis of a rotatable carousel. An indexing system rotates the carousel to selectively place one of the stack holding tubes in a treatment position. The improvement comprises a magnetizable member attached to the top of the stack of sample holders, a transfer tube having a bottom opening positioned to mate on top of the stack holding tube to hold the magnetizable member in a magnetic field, a device to raise and lower the magnetic coil about the transfer tube to raise and lower the magnetic coil about the transfer tube to raise the stack into the transfer tube allowing the carousel to be rotated, and lower the stack into another stack holding tube.

公开(公告)号：EP0154557A3

公开(公告)日：1988-02-03

申请号：EP85301579

申请日：1985-03-07

Applicant: Biomatics Inc.

Inventor： Gardos, Ivan

IPC: G01N01/28

CPC classification number: G01N1/31 ,  B05C3/05 ,  B05C13/02

Abstract: A magnetic lifting device for lifting a stack of specimen holders out of one tube and lowering them into another tube is disclosed. The device avoids the necessity of manual handling of the stack. ln the device there are a number of stack holding tubes, each one open at the top, positioned in a circle about a vertical axis of a rotatable carousel. An indexing system rotates the carousel to selectively place one of the stack holding tubes in a treatment position. The improvement comprises a magnetizable member attached to the top of the stack of sample holders, a transfer tube having a bottom opening positioned to mate on top of the stack holding tube to hold the magnetizable member in a magnetic field, a device to raise and lower the magnetic coil about the transfer tube to raise and lower the magnetic coil about the transfer tube to raise the stack into the transfer tube allowing the carousel to be rotated, and lower the stack into another stack holding tube.