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1. 发明专利

JP2013226104A Program for determining read error in base sequence 有权
标题翻译：用于确定基本序列读取错误的程序
公开(公告)号：JP2013226104A
公开(公告)日：2013-11-07
申请号：JP2012101755
申请日：2012-04-26
申请人： Natl Inst Of Radiological Sciences , 独立行政法人放射線医学総合研究所 , Maze:Kk , 株式会社メイズ
发明人： ABE MASUMI , KASAMA KOJI , YUNOKAWA HARUNOBU , SATO SHINJI , KONDO KAZUHIRO , HINAGATA TAKASHI
IPC分类号： C12Q1/68
CPC分类号： G06F19/22 , G06F19/24 , G06F19/70
摘要： PROBLEM TO BE SOLVED: To provide a program for determining whether the difference in base sequences is due to a read error or a mutation.SOLUTION: In step S101, a reference sequence and a first sequence of interest having homology to the reference sequence are obtained. In step S102, the edit distance between the reference sequence and the first sequence of interest is calculated. In step S103, for the first sequence of interest, a sequence of 3 or more consecutive identical bases is substituted for a sequence of 2 consecutive identical bases, and a second sequence of interest is made. In step S104, the edit distance of the second sequence of interest to the reference sequence substituted is calculated. In step S105, whether the difference is due to a read error or a mutation is determined on the basis of the calculated edit distance.
摘要翻译：要解决的问题：提供用于确定基本序列的差异是否是由于读取错误或突变引起的程序。解决方案：在步骤S101中，获得与参考序列具有同源性的参考序列和第一序列。在步骤S102中，计算参考序列与第一关注序列之间的编辑距离。在步骤S103中，对于第一感兴趣序列，将3个或更多个连续相同碱基的序列替换为2个连续相同碱基的序列，并且进行第二感兴趣的序列。在步骤S104中，计算第二感兴趣序列与被替换的参考序列的编辑距离。在步骤S105中，根据计算出的编辑距离来确定差异是由于读取错误还是突变。

2. 发明专利

JP2009193273A Method, apparatus, and program for analyzing expression of gene 有权
标题翻译：用于分析基因表达的方法，装置和程序
公开(公告)号：JP2009193273A
公开(公告)日：2009-08-27
申请号：JP2008032466
申请日：2008-02-13
申请人： Natl Inst Of Radiological Sciences , 独立行政法人放射線医学総合研究所
发明人： KASAMA KOJI , ABE MASUMI
IPC分类号： G06F19/00 , G06F19/20
摘要： PROBLEM TO BE SOLVED: To provide a method for easily comparing reference profile data (reference PD) with created measurement profile data (measurement PD) and analyzing an expression state of a gene. SOLUTION: The method includes a reference PD acquisition step S1 of showing, as a first waveform, a reference range of values equivalent to the number of bases based on positions and a detection amount of the values equivalent to the number of bases of DNA fragments, identifying and storing transcript seeds from which a predetermined peak in the first waveform comes, and acquiring the stored reference PD; a measurement PD creation step S2 of creating a measurement PD showing, as a second waveform, a measurement range of values equivalent to the number of bases obtained on the basis of positions and a detection amount of values equivalent to the number of bases of DNA fragments to be measured; a peak association step S3 applying correction processing and associating positions of peaks of a part of or all of at least either the first waveform or the second waveform; and a gene expression analyzing step S4 of reading information of the derivation of associated peak from transcript seed information, identifying the gene of the peak of the measurement PD, and thus, analyzing the expression state of the gene. COPYRIGHT: (C)2009,JPO&INPIT
摘要翻译：要解决的问题：提供一种用于将参考简档数据（参考PD）与创建的测量简档数据（测量PD）进行比较并分析基因的表达状态的方法。解决方案：该方法包括参考PD获取步骤S1，其作为第一波形，显示基于与基于位置的数量相等的碱基数的基准范围和相当于碱基数的碱基数的检测量 DNA片段，识别并存储来自第一波形中的预定峰值的转录物种子，并获取存储的参考PD; 创建测量PD的测量PD创建步骤S2，其显示作为第二波形的等效于基于与DNA片段的碱基数相当的位置和检测量获得的碱基数的测量范围待测峰值关联步骤S3，施加校正处理并将第一波形或第二波形中的至少一个的一部分或全部的峰值的位置相关联; 以及基因表达分析步骤S4，从转录子种子信息中读取相关峰的衍生信息，鉴定测定PD的峰的基因，从而分析基因的表达状态。版权所有（C）2009，JPO＆INPIT

3. 发明专利

JP2008226095A Gene expression variation analysis method, system and program 有权
标题翻译：基因表达变异分析方法，系统与程序
公开(公告)号：JP2008226095A
公开(公告)日：2008-09-25
申请号：JP2007066506
申请日：2007-03-15
申请人： Natl Inst Of Radiological Sciences , 独立行政法人放射線医学総合研究所
发明人： ABE MASUMI , KASAMA KOJI , KADOTA KOJI
IPC分类号： G06F19/00 , G06F19/20
摘要： PROBLEM TO BE SOLVED: To provide a method, system, or the like for processing a gene expression profile of a cDNA fragment coming from a transcript.
SOLUTION: An at least two-time measured gene expression profile is input as waveform data represented by peak information indicating at least an expressed transcript amount and a waveform position having the peak information, peak information interpolation extraction processing based on function approximation is applied to a plurality of pieces of the input waveform data, waveform correction based on waveform correction processing is performed among the plurality of pieces of waveform data including at least one waveform peak subjected to the interpolation extraction processing, waveform peak association processing for associating corresponding peaks on each waveform data is performed, and a result of the waveform peak association processing is output as a list together with a value indicating the expression amount of the transcript as a waveform peak list.
COPYRIGHT: (C)2008,JPO&INPIT
摘要翻译：待解决的问题：提供用于处理来自转录物的cDNA片段的基因表达谱的方法，系统等。输入至少两次测量的基因表达谱作为由表示至少表达转录物量的峰信息和具有峰信息的波形位置表示的波形数据，基于函数近似的峰信息插值提取处理是应用于多个输入波形数据，在包括经受内插提取处理的至少一个波形峰值的多个波形数据中进行基于波形校正处理的波形校正，用于将相应的峰值相关联的波形峰值关联处理在每个波形数据上进行，并且波形峰值关联处理的结果与表示誊本的表达量的值一起作为列表输出为波形峰值列表。版权所有（C）2008，JPO＆INPIT

4. 发明专利

JP2004259094A Method of improving precision of consensus sequence and method of determining consensus sequence using it 审中-公开
公开(公告)号：JP2004259094A
公开(公告)日：2004-09-16
申请号：JP2003050422
申请日：2003-02-27
申请人： Maze:Kk , 株式会社メイズ
发明人： YUNOKAWA HARUNOBU , KASAMA KOJI
IPC分类号： G06F17/30
摘要： PROBLEM TO BE SOLVED: To provide a method of improving the precision of a consensus sequence, simply heightening the precision of a consensus sequence more than the conventional method.
SOLUTION: According to this method of improving the precision of the consensus sequence, (1) the consensus sequence obtained on the basis of mRNA stored in a database and/or EST base sequence is compared with a genome sequence stored in a genome database by homology searching program. (2) Subsequently, by sequence of areas in the genome sequence found by the step (1), the area in the consensus sequence corresponding to the area is replaced.
COPYRIGHT: (C)2004,JPO&NCIPI

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