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/
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
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
16402463
Towards application/file-level characterization of block references: a case for fine-grained buffer management
Two contributions are made in this paper. First, we show that system level characterization of file block references is inadequate for maximizing buffer cache performance. We show that a finer-grained characterization approach is needed. Though application level characterization methods have been proposed, this is the first attempt, to the best of our knowledge, to consider file level characterizations. We propose an Application/File-level Characterization (AFC) scheme where we detect on-line the reference characteristics at the application level and then at the file level, if necessary. The results of this characterization are used to employ appropriate replacement policies in the buffer cache to maximize performance. The second contribution is in proposing an efficient and fair buffer allocation scheme. Application or file level resource management is infeasible unless there exists an allocation scheme that is efficient and fair. We propose the ΔHIT allocation scheme that takes away a block from the application/file where the removal results in the smallest reduction in the number of expected buffer cache hits. Both the AFC and ΔHIT schemes are on-line schemes that detect and allocate as applications execute. Experiments using trace-driven simulations show that substantial performance improvements can be made. For single application executions the hit ratio increased an average of 13 percentage points compared to the LRU policy, with a maximum increase of 59 percentage points, while for multiple application executions, the increase is an average of 12 percentage points, with a maximum of 32 percentage points for the workloads considered.
14211255
An Implementation Study of a Detection-Based Adaptive Block Replacement Scheme
In this paper, we propose a new adaptive buffer management scheme called DEAR (DEtection based Adaptive Replacement) that automatically detects the block reference patterns of applications and applies different replacement policies to different applications based on the detected reference pattern. The proposed DEAR scheme uses a periodic process. Detection is made by associating block attribute values such as backward distance and frequency gathered at the (i - 1)-th invocation with forward distances of blocks referenced between the (i - 1)-th and i-th invocations. We implemented the DEAR scheme in FreeBSD 2.2.5 and measured its performance using several real applications. The results show that compared with the LRU buffer management scheme, the proposed scheme reduces the number of disk I/Os by up to 51% (with an average of 23%) and the response time by up to 35% (with an average of 12%) in the case of single application executions. For multiple applications, the proposed scheme reduces the number of disk I/Os by up to 20% (with an average of 12%) and the over-all response time by up to 18% (with an average of 8%).
9363851
Design, Implementation, and Performance Evaluation of a Detection-Based Adaptive Block Replacement Scheme
A new buffer replacement scheme, called DEAR (detection-based adaptive replacement), is presented for effective caching of disk blocks in the operating system. The proposed DEAR scheme automatically detects block reference patterns of applications and applies different replacement policies to different applications depending on the detected reference pattern. The detection is made by a periodic process and is based on the relationship between block attribute values, such as backward distance and frequency gathered in a period, and the forward distance observed in the next period. This paper also describes an implementation and performance measurement of the DEAR scheme in FreeBSD. The results from performance measurements of several real applications show that, compared with the LRU scheme, the proposed scheme reduces the number of disk I/Os by up to 51 percent, and the response time by up to 35 percent in the case of single application executions. For multiple application executions, the results show that the proposed scheme reduces the number of disk I/Os by up to 20 percent and the overall response time by up to 18 percent.
5394476
Cross-Layer Analysis of Rate Adaptation, DCF and TCP in Multi-Rate WLANs
Wireless Internet access is facilitated by IEEE 802.11 WLANs that, in addition to realizing a specific form of CSMA/CA-distributed coordination function (DCF)- implement a range of performance enhancement features such as multi-rate adaptation that induce cross-layer protocol coupling. Recent works in empirical WLAN performance evaluation have shown that cross-layer interactions can be subtle, sometimes leading to unexpected outcomes. Two such instances are: significant throughput degradation (a bell-shaped throughput curve) resulting from automatic rate fallback (ARF) having difficulty distinguishing collision from channel noise, and scalable TCP performance over DCF that is able to curtail effective multiple access contention in the presence of many contending stations. The latter also mitigates the negative performance effect of ARF. In this paper, we present station-centric Markov chain models of WLAN cross-layer performance aimed at capturing complex interactions between ARF, DCF, and TCP. Our performance analyses may be viewed as multi-protocol extensions of Bianchi's IEEE 802.11 model that, despite significantly increased complexity, lead to tractable and accurate performance predictions due to modular coupling. Our results complement empirical and simulation-based findings, demonstrating the versatility and efficacy of station-centric Markov chain analysis for capturing cross-layer WLAN dynamics.
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.