25738322
GABI-Kat SimpleSearch: A Flanking Sequence Tag (FST) Database for the Identification of T-DNA Insertion Mutants in Arabidopsis Thaliana
SUMMARY
GABI-Kat SimpleSearch is a database of flanking sequence tags (FSTs) of T-DNA mutagenized Arabidopsis thaliana lines that were generated by the GABI-Kat project. Sequences flanking the T-DNA insertion sites were aligned to the A.thaliana genome sequence, annotated with information about the FST, the insertion site and the line from which the FST was derived. A web interface permits text-based as well as sequence-based searches for relevant insertions. GABI-Kat SimpleSearch aims to help biologists to quickly find T-DNA insertion mutants for their research.


AVAILABILITY
http://www.mpiz-koeln.mpg.de/GABI-Kat/
12311851
GABI-Kat SimpleSearch: an Arabidopsis thaliana T-DNA mutant database with detailed information for confirmed insertions
Insertional mutagenesis approaches, especially by T-DNA, play important roles in gene function studies of the model plant Arabidopsis thaliana. GABI-Kat SimpleSearch () is a Flanking Sequence Tag (FST)-based database for T-DNA insertion mutants generated by the GABI-Kat project. Currently, the database contains >108 000 mapped FSTs from ∼64 000 lines which cover 64% of all annotated A.thaliana protein-coding genes. The web interface allows searching for relevant insertions by gene code, keyword, line identifier, GenBank accession number of the FST, and also by BLAST. A graphic display of the genome region around the gene or the FST assists users to select insertion lines of their interests. About 3500 insertions were confirmed in the offspring of the plant from which the original FST was generated, and the seeds of these lines are available from the Nottingham Arabidopsis Stock Centre. The database now also contains additional information such as segregation data, gene-specific primers and confirmation sequences. This information not only helps users to evaluate the usefulness of the mutant lines, but also covers a big part of the molecular characterization of the insertion alleles.
26456568
Disclosure Analysis for Two-Way Contingency Tables
Disclosure analysis in two-way contingency tables is important in categorical data analysis. The disclosure analysis concerns whether a data snooper can infer any protected cell values, which contain privacy sensitive information, from available marginal totals (i.e., row sums and column sums) in a two-way contingency table. Previous research has been targeted on this problem from various perspectives. However, there is a lack of systematic definitions on the disclosure of cell values. Also, no previous study has been focused on the distribution of the cells that are subject to various types of disclosure. In this paper, we define four types of possible disclosure based on the exact upper bound and/or the lower bound of each cell that can be computed from the marginal totals. For each type of disclosure, we discover the distribution pattern of the cells subject to disclosure. Based on the distribution patterns discovered, we can speed up the search for all cells subject to disclosure.
18611349
Online Adaptive Fault-Tolerant Routing in 2D Torus
In this paper, we propose efficient routing algorithms for 2D torus with possible large number of faulty nodes. There is no presumption on the number and the distribution of faulty nodes. The proposed algorithms find a fault-free path between any two nonfaulty nodes with high probability in linear time by using only the local routing information of the network. The results of our empirical analysis through simulations show that the algorithms can find a fault-free path between any two nonfaulty nodes with high probability. For example, in a torus of size up to 128×128, where, the number of faulty nodes up to 15%, the heuristuc-square routing algorithm finds a fault-free path with a probability of 90% or higher. The experimental results are impressive for 2D torus with only four links per node.
1293275
Getting work done on the web: supporting transactional queries
Many searches on the web have a transactional intent. We argue that pages satisfying transactional needs can be distinguished from the more common pages that have some information and links, but cannot be used to execute a transaction. Based on this hypothesis, we provide a recipe for constructing a transaction annotator. By constructing an annotator with one corpus and then demonstrating its classification performance on another,we establish its robustness. Finally, we show experimentally that a search procedure that exploits such pre-annotation greatly outperforms traditional search for retrieving transactional pages.
2911701
Workload characterization of bioinformatics applications
The exponential growth in the amount of genomic information has spurred growing interest in large scale analysis of genetic data. Bioinformatics applications represent the increasingly important workloads. However, very few results on the behavior of these applications running on the state-of-the-art microprocessor and systems have been published. This paper proposes a suite of widely used bioinformatics applications and studies the execution characteristics of these benchmarks on a representative architecture-the Intel Pentium 4. To understand the impacts and implications of bioinformatics workloads on the microprocessor designs, we contrast the characteristics of bioinformatics workloads and the widely used SPEC 2000 integer benchmarks.
16207650
Term Disambiguation in Natural Language Query for XML
Converting a natural language query sentence into a formal database query is a major challenge. We have constructed NaLIX, a natural language interface for querying XML data. Through our experience with NaLIX, we find that failures in natural language query understanding can often be dealt with as ambiguities in term meanings. These failures are typically the result of either the user's poor knowledge of the database schema or the system's lack of linguistic coverage. With automatic term expansion techniques and appropriate interactive feedback, we are able to resolve these ambiguities. In this paper, we describe our approach and present results demonstrating its effectiveness.