31128018
The Repetitive Sequence Database and Mining Putative Regulatory Elements in Gene Promoter Regions
At least 43% of the human genome is occupied by repetitive elements. Moreover, around 51% of the rice genome is occupied by repetitive elements. The analysis of repetitive elements reveals that repetitive elements in our genome may have been very important in the evolutionary genomics. The first part of this study is to describe a database of repetitive elements - RSDB. The RSDB database contains repetitive elements, which are classified into the following categories: exact, tandem, and similar. The interfaces needed to query and show the results and statistical data, such as the relationship between repetitive elements and genes, cross-references of repetitive elements among different organisms, and so on, are provided. The second part of this study then attempts to mine the putative binding site for information on how combinations of the known regulatory sites and overrepresented repetitive elements in RSDB are distributed in the promoter regions of groups of functionally related genes. The overrepresented repetitive elements appearing in the associations are possible transcription factor binding sites. Our proposed approach is applied to Saccharomyces cerevisiae and the promoter regions of Yeast ORFs. The complete contents of RSDB and partial putative binding sites are available to the public at www.rsdb.csie.ncu.edu.tw. The readers may download partial query results.
12419359
Primer design for multiplex PCR using a genetic algorithm
Multiplex Polymerase Chain Reaction (PCR) experiments are used for amplifying several segments of the target DNA simultaneously and thereby to conserve template DNA, reduce the experimental time, and minimize the experimental expense. The success of the experiment is dependent on primer design. However, this can be a dreary task as there are many constrains such as melting temperatures, primer length, GC content and complementarity that need to be optimized to obtain a good PCR product. Motivated by the lack of primer design tools for multiplex PCR genotypic assay, we propose a multiplex PCR primer design tool using a genetic algorithm, which is a stochastic approach based on the concept of biological evolution, biological genetics and genetic operations on chromosomes, to find an optimal selection of primer pairs for multiplex PCR experiments. The presented experimental results indicate that the proposed algorithm is capable of finding a series of primer pairs that obeies the design properties in the same tube.
13750244
A database to aid probe design for virus identification
FENG-MAO LIN, HSIEN-DA HUANG, YU-CHUNG CHANG, PAK-LEONG CHAN, JORNG-TZONG HORNG, MING-TAT KO Department of Computer Science and Information Engineering, National Central University, No.300, Jungda Rd, Jhongli City, Taoyuan, Taiwan 320 ChungLi, 320, Taiwan Department of Biological Science and Technology & Institute of Bioinformatic, National ChiaoTung University, 1001 Ta Hsueh Road, Hsinchu, Taiwan 300 Hsin-Chu, 300, Taiwan Department of Biotechnology, Ming Chuan University, 250 Chung Shan North Road, Section 5, Taipei, 111, Taiwan Institute of Information Science, Academia Sinica, 128 Sec. 2, Academia Rd, Nankangm, Taipei, 115, Taiwan
5048088
KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites
KinasePhos is a novel web server for computationally identifying catalytic kinase-specific phosphorylation sites. The known phosphorylation sites from public domain data sources are categorized by their annotated protein kinases. Based on the profile hidden Markov model, computational models are learned from the kinase-specific groups of the phosphorylation sites. After evaluating the learned models, the model with highest accuracy was selected from each kinase-specific group, for use in a web-based prediction tool for identifying protein phosphorylation sites. Therefore, this work developed a kinase-specific phosphorylation site prediction tool with both high sensitivity and specificity. The prediction tool is freely available at .
7392928
Finding short DNA motifs using permuted markov models
Many short DNA motifs such as transcription factor binding sites (TFBS) and splice sites exhibit strong local as well as non-local dependence. We introduce permuted variable length Markov models (PVLMM) which could capture the potentially important dependencies among positions, and apply them to the problem of detecting splice and TFB sites. They have been satisfactory from the viewpoint of prediction performance, and also give ready biological interpretations of the sequence dependence observed. The issue of model selection is also studied.
5642826
A garbage-collecting typed assembly language
Typed assembly languages usually support heap allocation safely, but often rely on an external garbage collector to deallocate objects from the heap and prevent unsafe dangling pointers. Even if the external garbage collector is provably correct, verifying the safety of the interaction between TAL programs and garbage collection is nontrivial. This paper introduces a typed assembly language whose type system is expressive enough to type-check a Cheney-queue copying garbage collector, so that ordinary programs and garbage collection can co-exist and interact inside a single typed language. The only built-in types for memory are linear types describing individual memory words, so that TAL programmers can define their own object layouts, method table layouts, heap layouts, and memory management techniques.
17310261
Cross-cultural influences on women in the IT workforce
A review of 862 papers published in SIGMIS/CPR proceedings over the past 44 years revealed only 29 articles that focused on gender and the IT workforce or gender and IT education, the majority of which were presented at the 2003 conference whose theme was diversity in the IT workforce. Therefore, in response to the call for papers to extend our understanding of topics central to computer personnel research, we present data from our field study of gender and IT that is directed at understanding differing cross-cultural influences on female experiences in the IT workforce. Four themes emerged from analysis of data from four separate studies of women in the IT workforces in Australia, Ireland, New Zealand and the United States: motherhood and careers, career choice, family dynamics and gender stereotypes. Analysis of interviews with 167 women reveals a wide range of influences on women's choice of an IT career. These results lend empirical support to the individual differences theory of gender and IT as an alternative to essentialist or social construction theories.
10859494
Adaptive watermarking using relationships between wavelet coefficients
We propose an approach that hides watermarks in relationships between wavelet coefficients. This approach minimizes the perceptual distortion of watermarked images, measured by PSNR or just noticeable distortion (JND). Therefore, the strength of watermarks can be enlarged to increase the robustness of the watermarks, while keeping the quality of watermarked images visually acceptable. Experimental results show that the watermark is still detectable after common image processing operations such as JPEG compression, Gaussian filtering and sharpening.
3641866
The iProClass integrated database for protein functional analysis
Increasingly, scientists have begun to tackle gene functions and other complex regulatory processes by studying organisms at the global scales for various levels of biological organization, ranging from genomes to metabolomes and physiomes. Meanwhile, new bioinformatics methods have been developed for inferring protein function using associative analysis of functional properties to complement the traditional sequence homology-based methods. To fully exploit the value of the high-throughput system biology data and to facilitate protein functional studies requires bioinformatics infrastructures that support both data integration and associative analysis. The iProClass database, designed to serve as a framework for data integration in a distributed networking environment, provides comprehensive descriptions of all proteins, with rich links to over 50 databases of protein family, function, pathway, interaction, modification, structure, genome, ontology, literature, and taxonomy. In particular, the database is organized with PIRSF family classification and maps to other family, function, and structure classification schemes. Coupled with the underlying taxonomic information for complete genomes, the iProClass system (http://pir.georgetown.edu/iproclass/) supports associative studies of protein family, domain, function, and structure. A case study of the phosphoglycerate mutases illustrates a systematic approach for protein family and phylogenetic analysis. Such studies may serve as a basis for further analysis of protein functional evolution, and its relationship to the co-evolution of metabolic pathways, cellular networks, and organisms.