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    • 9. 发明授权
    • Sequence database search with sequence search trees
    • 序列数据库搜索与序列搜索树
    • US06633817B1
    • 2003-10-14
    • US09474929
    • 1999-12-29
    • Michael G. WalkerJames Z. WangEldar Y. Giladi
    • Michael G. WalkerJames Z. WangEldar Y. Giladi
    • G01N3348
    • G06F19/22G06F19/24
    • A method and system for generating and searching a tree-structured index of window vectors that represent database sequences comprise a window vector generation module, a tree-structured index generation module, a query sequence partitioning module, and a retrieval component. The window vector generation module partitions a database sequence into a plurality of overlapping windows. Each window has a fixed length W comprising a fixed number of nucleotides, and the offset among windows is determined by a parameter &Dgr;. The window vector generation module then maps each database sequence window into a window vector. The database sequence window vector indicates the frequency of appearance of each k-tuple in the corresponding database sequence window. The tree-structured index generation module then generates a tree-structured index using the database sequence window vectors. The query sequence partitioning module partitions a query sequence into a plurality of windows and maps each query sequence window into a query sequence window vector. Each query sequence window vector is then compared against the tree-structured index to locate the database sequences that are similar to the query sequence. The list of database sequences that are similar to the query sequence is then returned as the result of the search.
    • 用于生成和搜索表示数据库序列的窗口向量的树结构索引的方法和系统包括窗口向量生成模块,树结构索引生成模块,查询序列分区模块和检索组件。 窗口向量生成模块将数据库序列分割成多个重叠窗口。 每个窗口具有包含固定数目的核苷酸的固定长度W,并且窗口之间的偏移由参数Delta确定。 然后,窗口向量生成模块将每个数据库序列窗口映射到窗口向量中。 数据库序列窗口向量表示相应数据库序列窗口中每个k元组的出现频率。 然后,树结构索引生成模块使用数据库序列窗口向量生成树结构索引。 查询序列分区模块将查询序列分割成多个窗口,并将每个查询序列窗口映射到查询序列窗口向量中。 然后将每个查询序列窗口向量与树结构索引进行比较,以定位与查询序列相似的数据库序列。 作为搜索结果,返回与查询序列相似的数据库序列列表。