4,212 research outputs found
Matching Subsequences in Trees
Given two rooted, labeled trees and the tree path subsequence problem
is to determine which paths in are subsequences of which paths in . Here
a path begins at the root and ends at a leaf. In this paper we propose this
problem as a useful query primitive for XML data, and provide new algorithms
improving the previously best known time and space bounds.Comment: Minor correction of typos, et
Compressed Spaced Suffix Arrays
Spaced seeds are important tools for similarity search in bioinformatics, and
using several seeds together often significantly improves their performance.
With existing approaches, however, for each seed we keep a separate linear-size
data structure, either a hash table or a spaced suffix array (SSA). In this
paper we show how to compress SSAs relative to normal suffix arrays (SAs) and
still support fast random access to them. We first prove a theoretical upper
bound on the space needed to store an SSA when we already have the SA. We then
present experiments indicating that our approach works even better in practice
LRM-Trees: Compressed Indices, Adaptive Sorting, and Compressed Permutations
LRM-Trees are an elegant way to partition a sequence of values into sorted
consecutive blocks, and to express the relative position of the first element
of each block within a previous block. They were used to encode ordinal trees
and to index integer arrays in order to support range minimum queries on them.
We describe how they yield many other convenient results in a variety of areas,
from data structures to algorithms: some compressed succinct indices for range
minimum queries; a new adaptive sorting algorithm; and a compressed succinct
data structure for permutations supporting direct and indirect application in
time all the shortest as the permutation is compressible.Comment: 13 pages, 1 figur
Computer Aided Simulation of DNA Fingerprint Amplified Fragment Length Polymophism (AFLP) Using Suffix Tree Indexing and Data Mining
AFLP is one of the DNA Fingerprinting techniques which have broad application as genetic marker in various fields. Begin with the DNA sequence digestion using one or more particular restriction enzyme, ligation of the adapters to the overhanging sticky ends followed by DNA fragments amplification using PCR. The PCR reaction uses primers that match the adapter sequence and have some (1 to 3) dditional “selective” bases which could be any bases, this reduces the number of bands that will be amplified. Such technique intended to increase the amplified fragments peculiarity so the polymorphism of the organism being studied could be well visualized by gel electrophoresis. The computer aided of AFLP simulation developed in this research was aimed to predict this electrophoresis result by simulate the digestion, ligation and PCR process using some pattern recognition algorithm applied to the DNA sequence from online databases. Through this simulation the researcher
could determine the best combination of restriction enzyme and selective bases for their laboratory experiment. Suffix tree indexing was conducted during the exploration process of the genome sequence (in FASTA format) to find the restriction sites rapidly and create fragments of it. Data modeling enable the system draws the fragments into virtual DNA’s electrophoresis pattern. Data mining accomplish the simulation by exploring overall possible virtual DNA’s electrophoresis pattern and determine the best restriction enzyme and selective bases combination by calculating certain quantitative criteria
Faster Approximate String Matching for Short Patterns
We study the classical approximate string matching problem, that is, given
strings and and an error threshold , find all ending positions of
substrings of whose edit distance to is at most . Let and
have lengths and , respectively. On a standard unit-cost word RAM with
word size we present an algorithm using time When is
short, namely, or this
improves the previously best known time bounds for the problem. The result is
achieved using a novel implementation of the Landau-Vishkin algorithm based on
tabulation and word-level parallelism.Comment: To appear in Theory of Computing System
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