Nonrandom Clusters of Palindromes in Herpesvirus Genomes
Palindromes are symmetrical words of DNA in the sense that they read exactly the same as their reverse complementary sequences. Representing the occurrences of palindromes in a DNA molecule as points on the unit interval, the scan statistics can be used to identify regions of unusually high concentration of palindromes. These regions have been associated with the replication origins on a few herpesviruses in previous studies. However, the use of scan statistics requires the assumption that the points representing the palindromes are independently and uniformly distributed on the unit interval. In this paper, we provide a mathematical basis for this assumption by showing that in randomly generated DNA sequences, the occurrences of palindromes can be approximated by a Poisson process. An easily computable upper bound on the Wasserstein distance between the palindrome process and the Poisson process is obtained. This bound is then used as a guide to choose an optimal palindrome length in the analysis of a collection of 16 herpesvirus genomes. Regions harboring significant palindrome clusters are identified and compared to known locations of replication origins. This analysis brings out a few interesting extensions of the scan statistics that can help formulate an algorithm for more accurate prediction of replication origins.

title: Sensitivity analysis and efficient method for identifying optimal spaced seeds
abstract: 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.

title: Palindromes in SARS and Other Coronaviruses
abstract: 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.

title: Good spaced seeds for homology search
abstract: 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. 
 
 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.

title: Energy-aware MPEG-4 FGS streaming
abstract: In this paper, we propose an energy-aware MPEG-4 FGS video streaming system with client feedback. In this client-server system, the battery-powered mobile client sends its maximum decoding capability (i.e., its decoding aptitude) to the server in order to help the server determine the additional amount of data (in the form of enhancement layers on top of the base layer) per frame that it sends to the client, and thereby, set its data rate. On the client side, a dynamic voltage and frequency scaling technique is used to adjust the decoding aptitude of the client while meeting a constraint on the minimum achieved video quality. As a measure of energy efficiency of the video streamer, the notion of a normalized decoding load is introduced. It is shown that a video streaming system that maintains this normalized load at unity produces the optimum video quality with no energy waste. We implemented an MPEG-4 FGS video streaming system on an XScale-based testbed in which a server and a mobile client are wirelessly connected by a feedback channel. Based on the actual current measurements in this testbed, we obtain an average of 20% communication energy reduction in the client by making the MPEG-4 FGS streamer energy-aware.

title: Determining the specificity of terms using inside-outside information: a necessary condition of term hierarchy mining
abstract: This paper introduces new specificity measuring methods of terms using inside and outside information. Specificity of a term is the quantity of domain specific information contained in the term. Specific terms have a larger quantity of domain information than general terms. Specificity is an important necessary condition for building hierarchical relations among terms. If t1 is a hyponym of t2 in a domain term hierarchy, then the specificity of t1 is greater than that of t2. As domain specific terms are commonly compounds of the generic level term and some modifiers, inside information is important to represent the meaning of terms. Outside contextual information is also used to complement the shortcomings of inside information. We propose an information theoretic method to measure the quantity of terms. Experiments showed promising results with a precision of 73.9% when applied to terms in the MeSH thesaurus.

title: PLATCOM: a Platform for Computational Comparative Genomics
abstract: As more whole genome sequences become available, comparing multiple genomes at the sequence level can provide insight into new biological discovery. However, there are significant challenges for genome comparison. The challenge includes requirement for computational resources owing to the large volume of genome data. More importantly, since the choice of genomes to be compared is entirely subjective, there are too many choices for genome comparison. For these reasons, there is pressing need for bioinformatics systems for comparing multiple genomes where users can choose genomes to be compared freely.



PLATCOM (Platform for Computational Comparative Genomics) is an integrated system for the comparative analysis of multiple genomes. The system is built on several public databases and a suite of genome analysis applications are provided as exemplary genome data mining tools over these internal databases. Researchers are able to visually investigate genomic sequence similarities, conserved gene neighborhoods, conserved metabolic pathways and putative gene fusion events among a set of selected multiple genomes.



http://platcom.informatics.indiana.edu/platcom

title: Incremental cue phrase learning and bootstrapping method for causality extraction using cue phrase and word pair probabilities
abstract: This work aims to extract possible causal relations that exist between noun phrases. Some causal relations are manifested by lexical patterns like causal verbs and their sub-categorization. We use lexical patterns as a filter to find causality candidates and we transfer the causality extraction problem to the binary classification. To solve the problem, we introduce probabilities for word pair and concept pair that could be part of causal noun phrase pairs. We also use the cue phrase probability that could be a causality pattern. These probabilities are learned from the raw corpus in an unsupervised manner. With this probabilistic model, we increase both precision and recall. Our causality extraction shows an F-score of 77.37%, which is an improvement of 21.14 percentage points over the baseline model. The long distance causal relation is extracted with the binary tree-styled cue phrase. We propose an incremental cue phrase learning method based on the cue phrase confidence score that was measured after each causal classifier learning step. A better recall of 15.37 percentage points is acquired after the cue phrase learning.

title: PLATCOM: Current Status and Plan for the Next Stages
abstract: We have been developing a web-based system for comparing multiple genomes, PLATCOM, where users can choose genomes of their choice freely and perform analysis of the selected genomes with a suite of computational tools. PLATCOM is built on internal databases such as GenBank, COG, KEGG, and Pairwise Comparison Database (PCDB) that contains all pairwise comparisons (97,034 entries) of protein sequence files (.faa) and whole genome sequence files (.fna) of 312 replicons. Since combining multiple tools for sequence analysis requires a significant amount of programming work and knowledge on each tool, we also developed and incorporated high performance sequence data mining tools such as sequence clustering and neighborhood prediction. The next plan includes defining several data types for genome analysis and integrating system modules using data mining tools that operate on the genome data types. PLATCOM is available at http://platcom.informatics.indiana.edu.