465231
BLAST++: BLASTing queries in batches
UNLABELLED
BLAST++ is a tool that is integrated with NCBI BLAST, allowing multiple, say K, queries to be searched against a database concurrently. The results obtained by BLAST++ are identical to that obtained by executing BLAST on each of the K queries, but BLAST++ completes the processing in a much shorter time.


AVAILABILITY
http://xena1.ddns.comp.nus.edu.sg/~genesis/blast++


SUPPLEMENTARY INFORMATION
http://xena1.ddns.comp.nus.edu.sg/~genesis/blast++
16399618
Fast filter-and-refine algorithms for subsequence selection
Large sequence databases, such as protein, DNA and gene sequences in biology, are becoming increasingly common. An important operation on a sequence database is approximate subsequence matching, where all subsequences that are within some distance from a given query string are retrieved. This paper proposes a filter-and-refine algorithm that enables efficient approximate subsequence matching in large DNA sequence databases. It employs a bitmap indexing structure to condense and encode each data sequence into a shorter index sequence. During query processing, the bitmap index is used to filter out most of the irrelevant subsequences, and false positives are removed in the final refinement step. Analytical and experimental studies show that the proposed strategy is capable of reducing response time substantially while incurring only a small space overhead.
22168621
BLAST++ : A Tool for BLASTing Queries in Batches
BLAST is the standard tool that molecular biologists use to search for sequence similarity in genomic (and protein) databases. It employs a brute force approach of comparing a query sequence against every database sequence - for each pair of the sequences to be matched, BLAST searches for short fixed-length word pairs (seeds) in the sequences and then extends them to higher-scoring regions. To search multiple queries, the basic approach is to run BLAST on each of the queries one at a time. This is clearly inefficient and fails to exploit common subsequences that the collection of queries may share. In this paper, we propose a new genome search tool, BLAST++, that allows multiple, say K, queries to be searched against a database concurrently. The design of BLAST++ is based on our observation that the seed searching step of BLAST is a bottleneck that consumes more than 80% of the total response time! BLAST++ essentially treats a collection of queries as a single virtual query so that the seed searching step needs to be performed only once for common subsequences. We implemented BLAST++ as an extension of the NCBI BLAST, and evaluated its performance. Our study shows that the results obtained by BLAST++ are identical to that obtained by executing BLAST on each of the K queries, but the single-process version of BLAST++ completes the processing in a much shorter time, about only 25% of the original single-process version of NCBI BLAST.
7017728
Indexing Genomic Databases for Fast Homology Searching
Genomic sequence databases has been widely used by molecular biologists for homology searching. However, as amino acid and nucleotide databases are growing in size at an alarming rate, traditional brute force approach of comparing a query sequence against each of the database sequences is becoming prohibitively expensive. In this paper, we re-examine the problem of searching for homology in large protein databases. We proposed a novel filter-and-refine approach to speed up the search process. The scheme operates in two phases. In the filtering phase, a small set of candidate database sequences (as compared to all sequences in the database) is quickly identified. This is realized using a signature-based scheme. In the refinement phase, the query sequence is matched against the sequences in the candidate set using any local alignment strategies. Our preliminary experimental results show that the proposed method results in significant savings in computation without sacrificing on the accuracy of the answers as compared to FASTA.
20063786
Implementation of a graphics design framework on the Web
We propose a client-server graphics design framework and implement a room design system using CORBA. We have integrated technologies used in distributed computation (Java and CORBA) and computer graphics (VRML). To support multiuser collaborative design, we propose a supplier-consumer communication approach and implement it using the event service in CORBA. Our system can be applied in electronic commerce to improve the existing systems by allowing customers to select furniture and to visualize the whole furnished room in 3D.
10887794
Packet doppler: network monitoring using packet shift detection
Due to recent large-scale deployments of delay and loss-sensitive applications, there are increasingly stringent demands on the monitoring of service level agreement metrics. Although many end-to-end monitoring methods have been proposed, they are mainly based on active probing and thus inject measurement traffic into the network. In this paper, we propose a new scheme for monitoring service level agreement metrics, in particular, delay distribution. Our scheme is passive and therefore will not cause perturbation to real traffic. Using realistic delay and traffic demands, we show that our scheme achieves high accuracy and can detect burst events that will be missed by probing based methods.
3219653
Key Elements Tracing Method for Parallel XML Parsing in Multi-Core System
Though XML is applied intensively in a lot of applications, XML parsing is not practical in many fields because of its poor performance. Parallel XML parsing on multi-core is a promising choice. Previous methods all adopt data parallel approach on XML parsing. As the semi-structured nature of XML, they were obliged to divide the data into well-formed XML chunks and then parse these chunks parallel. The division process is named as preparsing. As the preparsing is serial, it becomes the bottleneck of parallel XML parsing. Related work Simultaneous Finite Transducer (SFTXP) parallelized the preparsing stage. It maintained multiple preparser results for each equal sized chunk according to enumerated all possible parsing states. In spite of finite states for each XML, the overhead by SFTXP is tremendous, including CPU time and memory for multiple results generating and storing, respectively. In this work, we address parallel XML parsing by Key Element Parse Tracing (KEPT) method which parallelizes the preparsing and parsing at element level. It remolds the preparsing as a key element extracting process and schedules the processing of key elements in the framework of KEPT. Then parsing process is parallelized as a whole. To demonstrate the effectiveness, we implement it on libxml2 and obtain good scalability on both an 8-core Linux machine and an 8-core 24 SMT Sun machine running Solaris.
12667544
Camera Readable 2D Bar Codes Design and Decoding for Mobile Phones
2D bar codes were designed to carry significantly more data than its 1D counterpart. Thanks to the popular combination of cameras and mobile phones, it will naturally bring great commercial value to use the camera phone for 2D bar code reading. This paper addresses the problem of specific 2D bar code design for mobile phones and introduces a low-level solution of matrix codes. At the same time, we propose an efficient scheme for 2D bar codes decoding, of which the effort is put on solutions of the difficulties introduced by low image quality that is very common in bar code images taken by a phone camera.
1622406
Structure Analysis and SNR-Variance Evolution for Parallel Concatenated Coded IDMA Systems
This paper is concerned with parallel concatenated coded interleave-division multiple-access (IDMA) systems. We briefly present the transmitter/receiver structure of these systems and propose an efficient SNR-variance evolution scheme for bit-error-rate (BER) performance evaluation. The proposed evolution scheme is also useful for system performance optimization. Numerical results show that the BER performance curves obtained by simulation and evolution are quite close when the data length is long enough.
5812455
Knowledge Enhanced IT Service Management
To manage the increasing complexity of IT systems and align IT services with business is the main theme of IT Service Management (ITSM). Current ITSM architecture adopts ITU as the framework to integrate silos of operational management tools and configuration information to build an end-to-end solution based on best practices. However, it lacks of a systematic means to address an important aspect of IT operation, i.e., managing the knowledge separated in various tools and experts' minds. In this paper, a novel knowledge-enhanced architecture is proposed to improve the effectiveness and efficiency of ITSM. The essential contribution of this novel architecture is to involve a Knowledge Management Database (KMDB) which provides assistance for knowledge capture, mining, storage and sharing. The paper will discuss an approach of how to construct such a KMDB with motivating scenarios and detailed description of key components. To validate the approach, a prototype system is developed and evaluated by being applied for problem analysis on a Cisco Voice over IP (VoIP) system. The experiment results show a remarkable improvement in the effectiveness and efficiency for practical IT service management operations.