20405083
GAME: A simple and efficient whole genome alignment method using maximal exact match filtering
In this paper, we present a simple and efficient whole genome alignment method using maximal exact match (MEM). The major problem with the use of MEM anchor is that the number of hits in non-homologous regions increases exponentially when shorter MEM anchors are used to detect more homologous regions. To deal with this problem, we have developed a fast and accurate anchor filtering scheme based on simple match extension with minimum percent identity and extension length criteria. Due to its simplicity and accuracy, all MEM anchors in a pair of genomes can be exhaustively tested and filtered. In addition, by incorporating the translation technique, the alignment quality and speed of our genome alignment algorithm have been further improved. As a result, our genome alignment algorithm, GAME (Genome Alignment by Match Extension), performs competitively over existing algorithms and can align large whole genomes, e.g., A. thaliana, without the requirement of typical large memory and parallel processors. This is shown using an experiment which compares the performance of BLAST, BLASTZ, PatternHunter, MUMmer and our algorithm in aligning all 45 pairs of 10 microbial genomes. The scalability of our algorithm is shown in another experiment where all pairs of five chromosomes in A. thaliana were compared.
16784503
PhyloDraw: a phylogenetic tree drawing system
UNLABELLED
PhyloDraw is a unified viewing tool for phylogenetic trees. PhyloDraw supports various kinds of multi-alignment formats (Dialign2, Clustal-W, Phylip format, NEXUS, MEGA, and pairwise distance matrix) and visualizes various kinds of tree diagrams, e.g. rectangular cladogram, slanted cladogram, phylogram, unrooted tree, and radial tree. By using several control parameters, users can easily and interactively manipulate the shape of phylogenetic trees. This program can export the final tree layout to BMP (bitmap image format) and PostScript.


AVAILABILITY
http://pearl.cs.pusan.ac.kr/phylodraw/


CONTACT
jhchoi@pearl.cs.pusan.ac.kr
10262654
COMPAM : visualization of combining pairwise alignments for multiple genomes
UNLABELLED
COMPAM is a tool for visualizing relationships among multiple whole genomes by combining all pairwise genome alignments. It displays shared conserved regions (blocks) and where these blocks occur (edges) as block relation graphs which can be explored interactively. An unannotated genome, e.g. can then be explored using information from well-annotated genomes, COG-based genome annotation and genes. COMPAM can run either as a stand-alone application or through an applet that is provided as service to PLATCOM, a toolset for whole genome comparative analysis, where a wide variety of genomes can be easily selected. Features provided by COMPAM include the ability to export genome relationship information into file formats that can be used by other existing tools.


AVAILABILITY
http://bio.informatics.indiana.edu/projects/compam/
351981
Real-time Animation Technique for Flexible and Thin Objects
In this paper, we propose an e cient technique for the animation of exible thin objects. Massspring model was employed to represent the exible objects. Many techniques have used the mass-spring model to generate plausible animation of soft objects. The easiest approach to animation with mass-spring model is explicit Euler method, but the explicit Euler method has serious disadvantage that it su ers from `instability problem'. The implicit integration method is a possible solution to overcome the instability problem. However, the most critical aw of the implicit method is that it involves a large linear system. This paper presents a fast animation technique for mass-spring model with approximated implicit method. The proposed technique stably updates the state of n mass-points in O(n) time when the number of total springs are O(n). We also consider the interaction of the exible object and air in order to generate plausible results.
6230675
ARCS: an aggregated related column scoring scheme for aligned sequences
MOTIVATION
Biologists frequently align multiple biological sequences to determine consensus sequences and/or search for predominant residues and conserved regions. Particularly, determining conserved regions in an alignment is one of the most important activities. Since protein sequences are often several-hundred residues or longer, it is difficult to distinguish biologically important conserved regions (motifs or domains) from others. The widely used tools, Logos, Al2co, Confind, and the entropy-based method, often fail to highlight such regions. Thus a computational tool that can highlight biologically important regions accurately will be highly desired.


RESULTS
This paper presents a new scoring scheme ARCS (Aggregated Related Column Score) for aligned biological sequences. ARCS method considers not only the traditional character similarity measure but also column correlation. In an extensive experimental evaluation using 533 PROSITE patterns, ARCS is able to highlight the motif regions with up to 77.7% accuracy corresponding to the top three peaks.


AVAILABILITY
The source code is available on http://bio.informatics.indiana.edu/projects/arcs and http://goldengate.case.edu/projects/arcs
2374761
Tamper-Evident Digital Signature Protecting Certification Authorities Against Malware
We introduce the notion of tamper-evidence for digital signature generation in order to defend against attacks aimed at covertly leaking secret information held by corrupted signing nodes. This is achieved by letting observers (which need not be trusted) verify the absence of covert channels by means of techniques we introduce herein. We call our signature schemes tamper-evident since any deviation from the protocol is immediately detectable. We demonstrate our technique for the RSA-PSS (known as RSA's probabilistic signature scheme) and DSA signature schemes and show how the same technique can be applied to the Schnorr and Feige-Fiat-Shamir (FFS) signature schemes. Our technique does not modify the distribution of the generated signature transcripts, and has only a minimal overhead in terms of computation, communication, and storage
16402380
The specification and schedulability analysis of real-time systems using ACSR
To engineer reliable real-time systems, it is desirable to detect timing anomalies early in the development process. However, there is little work addressing the problem of accurately predicting timing properties of real-time systems before implementations are developed. This paper describes an approach to the specification and schedulability analysis of real-time systems based on the timed process algebra ACSR-VP, which is an extension of algebra of communicating shared resources (ACSR) with value-passing communication and dynamic priorities. Combined with the existing features of ACSR for representing time, synchronization and resource requirements, ACSR-VP is capable of specifying a variety of real-time systems with different scheduling disciplines in a modular fashion. Moreover, we can perform schedulability analysis on real-time systems specified in ACSR-VP automatically by checking for a certain bisimulation relation.
926635
Escape analysis for Java
This paper presents a simple and efficient data flow algorithm for escape analysis of objects in Java programs to determine (i) if an object can be allocated on the stack; (ii) if an object is accessed only by a single thread during its lifetime, so that synchronization operations on that object can be removed. We introduce a new program abstraction for escape analysis, the connection graph, that is used to establish reachability relationships between objects and object references. We show that the connection graph can be summarized for each method such that the same summary information may be used effectively in different calling contexts. We present an interprocedural algorithm that uses the above property to efficiently compute the connection graph and identify the non-escaping objects for methods and threads. The experimental results, from a prototype implementation of our framework in the IBM High Performance Compiler for Java, are very promising. The percentage of objects that may be allocated on the stack exceeds 70% of all dynamically created objects in three out of the ten benchmarks (with a median of 19%), 11% to 92% of all lock operations are eliminated in those ten programs (with a median of 51%), and the overall execution time reduction ranges from 2% to 23% (with a median of 7%) on a 333 MHz PowerPC workstation with 128 MB memory.
15197780
Interprocedural pointer alias analysis
We present practical approximation methods for computing and representing interprocedural aliases for a program written in a language that includes pointers, reference parameters, and recursion. We present the following contributions: (1) a framework for interprocedural pointer alias analysis that handles function pointers by constructing the program call graph while alias analysis is being performed; (2) a flow-sensitive interprocedural pointer alias analysis algorithm; (3) a flow-insensitive interprocedural pointer alias analysis algorithm; (4) a flow-insensitive interprocedural pointer alias analysis algorithm that incorporates kill information to improve precision; (5) empirical measurements of the efficiency and precision of the three interprocedural alias analysis algorithms.
16977036
Element-Free Elastic Models for Volume Fitting and Capture
We present a new method of fitting an element-free volumetric model to a sequence of deforming surfaces of a moving object. Given a sequence of visual hulls, we iteratively fit an element-free elastic model to the visual hull in order to extract the optimal pose of the captured volume. The fitting of the volumetric model is acheived by minimizing a combination of elastic potential energy, a surface distance measure, and a self-intersection penalty for each frame. A unique aspect of our work is that the model is mesh free - since the model is represented as a point cloud, it is easy to construct, manipulate and update the model as needed. Additionally, linear elasicity with rotation compensation makes it possible to handle local deformations and large rotations of body parts much more efficiently than other volume fitting approaches. Our experimental results for volume fitting and capture in a multi-view camera setting demonstrate the robustness of element-free elastic models against noise and self-occlusions.