SUMMARY We have developed STAN (suffix-tree analyser), a tool to search for nucleotidic and peptidic patterns within whole chromosomes. Pattern syntax uses a string variable grammar-like formalism which allows the description of complex patterns including ambiguities, insertions/deletions, gaps, repeats and palindromes. STAN is based on a reduction to multipart matching on a suffix-tree data st...

Indexing n-gram phrases from text has many practical applications. Plagiarism detection, comparison of DNA of sequence or spam detection. In this paper we describe several data structures like hash table or B+ tree that could store n-grams for searching. We perform tests that shows their advantages and disadvantages. One of neglected data structure for this purpose, ternary search tree, is deep...

Primary B-tree, a variant of B-tree structure with row data in leaf blocks, is an ideal storage organization for queries involving exact match and/or range search on primary keys. Commercially, primary B-tree like structures have been supported in DBMSs like Compaq Non-Stop SQL, Sybase Adaptive Server, and Microsoft SQL Server. Oracle’s index-organized table is like a primary B-tree; however, i...

Gromov hyperbolicity of a metric space measures the distance from perfect tree-like structure. The measure has “worst-case” aspect to it, in sense that it detects region which sees maximum deviation In this article we introduce an “average-case” version hyperbolicity, whether “most space”, with respect given probability measure, looks like tree. main result paper is if average small, then can b...

This paper proposes a video structure matching framework based on a tree matching algorithm which can be used as an effective video retrieval tool in a media management system. We define two types of specialized tree matching algorithms. The first is the non-ordered tree matching and the second is the ordered tree matching. The first algorithm is not constrained by the temporal ordering of the ...

We give an analogue of the Riis Complexity Gap Theorem for Quantified Boolean Formulas (QBFs). Every first-order sentence φ without finite models gives rise to a sequence of QBFs whose minimal refutations in tree-like QResolution are either of polynomial size (if φ has no models) or at least exponential in size (if φ has some infinite model). However, differently from the translations to propos...

Vertebrate lung has tree-like structure which facilitates gas exchange. After discovery of the involvement of several key toolkit genes--FGF10, BMP4, and Shh, huge amount of molecular information on lung development is now available. However, how their interactions result in a branched structure has not been elucidated. Recently, some studies have utilized mathematical models to understand the ...

We propose a monitoring mechanism for recording the evolution of systems after certain computations, maintaining the history in a tree-like structure. Technically, we develop the monitoring mechanism in a variant of ADR (after Architectural Design Rewriting), a rule-based formal framework for modelling the evolution of architectures of systems. The hierarchical nature of ADR allows us to take f...