17801469
Sensitivity analysis and efficient method for identifying optimal spaced seeds
The novel introduction of spaced seed idea in the filtration stage of sequence comparison by Ma et al. (Bioinformatics 18 (2002) 440) has greatly increased the sensitivity of homology search without compromising the speed of search. Finding the optimal spaced seeds is of great importance both theoretically and in designing better search tool for sequence comparison. In this paper, we study the computational aspects of calculating the hitting probability of spaced seeds; and based on these results, we propose an efficient algorithm for identifying optimal spaced seeds.
64851
Palindromes in SARS and Other Coronaviruses
With the identification of a novel coronavirus associated with the severe acute respiratory syndrome (SARS), computational analysis of its RNA genome sequence is expected to give useful clues to help elucidate the origin, evolution, and pathogenicity of the virus. In this paper, we study the collective counts of palindromes in the SARS genome along with all the completely sequenced coronaviruses. Based on a Markov-chain model for the genome sequence, the mean and standard deviation for the number of palindromes at or above a given length are derived. These theoretical results are complemented by extensive simulations to provide empirical estimates. Using a z score obtained from these mathematical and empirical means and standard deviations, we have observed that palindromes of length four are significantly underrepresented in all the coronaviruses in our data set. In contrast, length-six palindromes are significantly underrepresented only in the SARS coronavirus. Two other features are unique to the SARS sequence. First, there is a length-22 palindrome TCTTTAACAAGCTTGTTAAAGA spanning positions 25962-25983. Second, there are two repeating length-12 palindromes TTATAATTATAA spanning positions 22712-22723 and 22796-22807. Some further investigations into possible biological implications of these palindrome features are proposed.
53306290
Good spaced seeds for homology search
Motivation: Filtration is an important technique used to speed up local alignment as exemplified in the BLAST programs. Recently, Ma et al. discovered that better filtering can be achieved by spacing out the matching positions according to a certain pattern, instead of contiguous positions to trigger a local alignment in their PatternHunter program. Such a match pattern is called a spaced seed. 
 
Results: Our numerical computation shows that the ranks of spaced seeds (based on sensitivity) change with the sequences similarity. Since homologous sequences may have diverse similarity, we assess the sensitivity of spaced seeds over a range of similarity levels and present a list of good spaced seeds for facilitating homology search in DNA genomic sequences. We validate that the listed spaced seeds are indeed more sensitive using three arbitrarily chosen pairs of DNA genomic sequences.
9907674
Multiple Genome Alignment by Clustering Pairwise Matches
We have developed a multiple genome alignment algorithm by using a sequence clustering algorithm to combine local pairwisegenome sequence matches produced by pairwise genome alignments, e.g, BLASTZ. Sequence clustering algorithms often generate clusters of sequences such that there exists a common shared region among all sequences in each cluster. To use a sequence clustering algorithm for genome alignment, it is necessary to handle numerous local alignments between a pair of genomes. We propose a multiple genome alignment method that converts the multiple genome alignment problem to the sequence clustering problem. This method does not need to make a guide tree to determine the order of multiple alignment, and it accurately detects multiple homologous regions. As a result, our multiple genome alignment algorithm performs competitively over existing algorithms. This is shown using an experiment which compares the performance of TBA, MultiPipMaker (MPM) and our algorithm in aligning 12 groups of 56 microbial genomes and by evaluating the number of common COGs detected.
33820430
PA-ZSA (Power-Aware Zero-Slack Algorithm): A Graph-Based Timing Analysis for Ultra-Low Power CMOS VLSI
This paper describes a slack budget distribution algorithm for ultra-low power CMOS logic circuits in a VLSI design environment. We introduce Power-Aware Zero-Slack Algorithm (PA-ZSA), which distributes the surplus time slacks into the most power-hungry modules. The PA-ZSA ensures that the total slack budget is near-maximal and the total power is minimal as a power-aware version of the well-known zero-slack algorithm (ZSA). Based on these time slacks, we have conducted the low-power optimization at gate level by using technology scaling technique. The experimental results show that our strategy reduces average 36% of the total (static and dynamic) power over the conventional slack budget distribution algorithms.
11243606
A Workbench for Acquiring Semantic Information and Constructing Dictionary for Compound Noun Analysis
This paper describes a workbench system for constructing a dictionary to interpret compound nouns, which integrates the acquisition of semantic information and interpretation of compound nouns. First, we extract semantic information from a machine readable dictionary and corpora using regular expressions. Then, the semantic relation of compound nouns are interpreted based on semantic relations, semantic features extracted automatically, and subcategorization information according to the characteristics of a head noun, i.e. attributive or predicative. Experimental results show that our method using hybrid knowledge depending on the characteristics of a head noun improves the accuracy rate by 40.30% and the coverage rate by 12.73% better than previous researches using semantic relations extracted from MRDs. As compound nouns are highly productive and their interpretation requires hybrid knowledge, we propose a workbench for compound noun interpretation in which necessary knowledge such as semantic patterns, semantic relations, and interpretation instances can be extended, rather than assuming a pre-defined lexical knowledge.
762901
A Statistical Model for Automatic Extraction of Korean Transliterated Foreign Words
In this paper, we will describe a Korean transliterated foreign word extraction algorithm. In the proposed method, we reformulate the foreign word extraction problem as a syllable-tagging problem such that each syllable is tagged with a foreign syllable tag or a pure Korean syllable tag. Syllable sequences of Korean strings are modelled by Hidden Markov Model whose state represents a character with binary marking to indicate whether the syllable is part of a transliterated foreign word or not. The proposed method extracts a transliterated foreign word with high recall rate and precision rate. Moreover, our method shows good performance even with small-sized training corpora.
8177740
Energy-Aware Wireless Video Streaming
This paper presents a dynamic energy management policy for a wireless video streaming system, consisting of battery-powered client and server. The paper starts from the observation that the video quality in wireless streaming is a function of three factors: encoding aptitude of the server, decoding aptitude of the client, and the wireless channel. Based on this observation, the energy consumption of a wireless video streaming system is modeled and analyzed. Using the proposed model, the optimal energy assignment to each video frame is done such that the maximum system lifetime is achieved while satisfying a given minimum video quality requirement. Experimental results show that the proposed policy increases the system lifetime by 20%.