Quadtree Representation of DNA Sequences

نویسندگان

  • Natsuhiro Ichinose
  • Tetsushi Yada
  • Toshihisa Takagi
چکیده

Quadtree representation is a method representing a frequency distribution of all oligo nucleotides in long DNA sequences. The method is theoretically equivalent to chaos game representation [2, 3], which represents orbits of the chaos game system (or iterated function system [1]) driven by the DNA sequences. Since the relation between a point in the orbit and a subsequence in the driving DNA sequences is continuous and one-to-one [1], the frequency distribution of the orbit is equivalent to that of successive nucleotides. Figure 1 shows an example of the configuration of 2-mer nucleotides in the quadtree representation. In the configuration the frequency of each 2-mer will be represented on the corresponding area by color or gray scale. Each 2-mer is hierarchically arranged: namely the first nucleotide in the bottom-left 4 areas corresponds to “A”, the bottom-right areas correspond to “G”, the top-left areas correspond to “C” and the top-right areas correspond to “T”. The area corresponding to each first nucleotide is divided in four, then each second nucleotide is assigned to a divided area by the same way. If the distribution of the 3-mer or longer nucleotides is considered, furthermore each area is divided in four and each nucleotide is assigned to one of them hierarchically. CC CT

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Motion Estimation with Quadtree Splines

This paper presents a motion estimation algorithm based on a new multiresolution representation, the quadtree spline. This representation describes the motion field as a collection of smoothly connected patches of varying size, where the patch size is automatically adapted to the complexity of the underlying motion. The topology of the patches is determined by a quadtree data structure, and bot...

متن کامل

Motion Estimation with Quadtree Splines - Pattern Analysis and Machine Intelligence, IEEE Transactions on

This paper presents a motion estimation algorithm based on a new multiresolution representation, the quadtree spline. This representation describes the motion field as a collection of smoothly connected patches of varying size, where the patch size is automatically adapted to the complexity of the underlying motion. The topology of the patches is determined by a quadtree data structure, and bot...

متن کامل

Data Structures for Quadtree

A number of data structures for representing images by quadtrees without pointers are discussed. The image is treated as a collection of leaf nodes. Each leaf node is represented by use of a locational code corresponding to a sequence of directional codes that locate the leaf along a path from the root of the tree. Somewhat related is the concept of a forest which is a representation that consi...

متن کامل

Quadtree Representation & Compression of Spatial Data

Spatial data representation and compression has become a focus issue in computer graphics and image processing applications. Quadtrees, as one of hierarchical data structures, basing on the principle of recursive decomposition of space, always offer a compact and efficient representation of an image. For a given image, the choice of quadtree root node plays an important role in its quadtree rep...

متن کامل

A polygon soup representation for multiview coding

This paper presents a polygon soup representation for multiview data. Starting from a sequence of multi-view video plus depth (MVD) data, the proposed quad-based representation takes into account, in a unified manner, different issues such as compactness, compression, and intermediate view synthesis. The representation is extracted from MVD data in two steps. First, a set of 3D quads is extract...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

عنوان ژورنال:

دوره   شماره 

صفحات  -

تاریخ انتشار 2001