205231250
The Universal Protein Resource (UniProt)
The ability to store and interconnect all available information on proteins is crucial to modern biological research. Accordingly, the Universal Protein Resource (UniProt) plays an increasingly important role by providing a stable, comprehensive, freely accessible central resource on protein sequences and functional annotation. UniProt is produced by the UniProt Consortium, formed in 2002 by the European Bioinformatics Institute (EBI), the Protein Information Resource (PIR) and the Swiss Institute of Bioinformatics (SIB). The core activities include manual curation of protein sequences assisted by computational analysis, sequence archiving, development of a user-friendly UniProt web site and the provision of additional value-added information through cross-references to other databases. UniProt is comprised of three major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase and the UniProt Reference Clusters. An additional component consisting of metagenomic and environmental sequences has recently been added to UniProt to ensure availability of such sequences in a timely fashion. UniProt is updated and distributed on a bi-weekly basis and can be accessed online for searches or download at .
197229
The PIR integrated protein databases and data retrieval system
The Protein Information Resource (PIR) provides many databases and tools to support genomic and proteomic research. PIR is a member of UniProt—Universal Protein Resource—the central repository of protein sequence and function, which maintains UniProt Knowledgebase with extensively curated annotation, UniProt Reference databases to speed sequence searches, and UniProt Archive to reflect sequence history. PIR also provides PIRSF family classification system based on evolutionary relationships of full-length proteins, and iProClass integrated database of protein family, function, and structure. These databases are easily accessible from PIR web site using a centralized data retrieval system for information retrieval and knowledge discovery.
7951451
A New Test System for Stability Measurement of Marker Gene Selection in DNA Microarray Data Analysis
Microarray gene expression data contains informative features that reflect the critical processes controlling prominent biological functions. Feature selection algorithms have been used in previous biomedical research to find the “marker” genes whose expression value change corresponds to the most eminent difference between specimen classes. One problem encountered in such analysis is the imbalance between very large numbers of genes versus relatively fewer specimen samples. A common concern, therefore, is “overfitting” the data and deriving a set of marker genes with low stability over the entire set of possible specimens. To address this problem, we propose a new test environment in which synthetic data is perturbed to simulate possible variations in gene expression values. The goal is for the generated data to have appropriate properties that match natural data, and that are appropriate for use in testing the sensitivity of feature selection algorithms and validating the robustness of selected marker genes. In this paper, we evaluate a statistically-based resampling approach and a Principal Components Analysis (PCA)-based linear noise distribution approach. Our results show that both methods generate reasonable synthetic data and that the signal/noise rate (with variation weights at 5%, 10%, 20% and 30%) measurably impacts the classification accuracy and the marker genes selected. Based on these results, we identify the most appropriate marker gene selection and classification techniques for each type and level of noise we modeled.
12033624
Computing motif correlations in proteins
Protein motifs, which are specific regions and conserved regions, are found by comparing multiple protein sequences. These conserved regions in general play an important role in protein functions and protein folds, for example, for their binding properties or enzymatic activities. The aim here is to find the existence correlations of protein motifs. The knowledge of protein motif/domain sharing should be important in shedding new light on the biologic functions of proteins and offering a basis in analyzing the evolution in the human genome or other genomes. The protein sequences used here are obtained from the PIR-NREF database and the protein motifs are retrieved from the PROSITE database. We apply data mining approach to discover the occurrence correlations of motif in protein sequences. The correlation of motifs mined can be used in evolution analyses and protein structure prediction. We discuss the latter, i.e., protein structure prediction in this study. The correlations mined are stored and maintained in a database system. The database is now available at http://bioinfo.csie.ncu.edu.tw/ProMotif/.
15014203
A VQ-based image-in-image data hiding scheme
Vector quantization (VQ)-based data hiding and watermarking techniques form a newly developed branch in the digital watermarking research field. We propose a novel watermarking scheme for image-in-image data hiding based on VQ. Unlike existing schemes in the literature for embedding a binary watermark into the original image with VQ, we present an efficient and secure algorithm for embedding a gray-level watermark into the original. The offered scheme is robust to attacks such as VQ compression and JPEG compression. Moreover, it greatly expands the capacity of the watermarking system. Experimental results demonstrate the superiority of our scheme in watermark robustness and watermark capacity. The results also prove the effectiveness of our proposed schemes in VQ-based image-in-image data hiding.
1404678
SpliceInfo: an information repository for mRNA alternative splicing in human genome
We have developed an information repository named SpliceInfo to collect the occurrences of the four major alternative-splicing (AS) modes in human genome; these include exon skipping, 5′-alternative splicing, 3′-alternative splicing and intron retention. The dataset is derived by comparing the nucleotide and protein sequences available for a given gene for evidence of AS. Additional features such as the tissue specificity of the mRNA, the protein domain contained by exons, the GC-ratio of exons, the repeats contained within the exons, and the Gene Ontology are annotated computationally for each exonic region that is alternatively spliced. Motivated by a previous investigation of AS-related motifs such as exonic splicing enhancer and exonic splicing silencer, this resource also provides a means of identifying motifs candidates and this should help to identify potential regulatory mechanisms within a particular exonic sequence set and its two flanking intronic sequence sets. This is carried out using motif discovery tools to identify motif candidates related to alternative splicing regulation and together with a secondary structure prediction tool, will help in the identification of the structural properties of such regulatory motifs. The integrated resource is now available on http://SpliceInfo.mbc.NCTU.edu.tw/.
45740416
Automated Information Mining on Multimedia TV News Archives
This paper addresses an integrated information mining techniques for multimedia TV-news archive. The utilizes techniques from the fields of acoustic, image, and video analysis, for information retrieval on news story title, newsman and scene identification. The goal is to construct a compact yet meaningful abstraction of broadcast news video, allowing users to browse through large amounts of data in a non-linear fashion with flexibility and efficiency. By using acoustic analysis, the system can classify video into news versus commercials, with 90% accuracy on a data set of 400 hours TV-news recorded off the air from July 2003 to August of 2004. By applying speaker identification and/or image detection techniques, each news stories can be segmented with an accuracy of 96%. On screen captions or subtitles are recognized by OCR techniques to produce the text title of each news stories. The extracted title words can be used to link or to navigate more related News contents on the WWW. In cooperation with facial and scene analysis and recognition techniques, OCR results can provide users with multimodality query for specific news stories. Some experimental results are presented and discussed for the system reliability and performance evaluation and comparison.