6603995
Protein family classification and functional annotation
With the accelerated accumulation of genomic sequence data, there is a pressing need to develop computational methods and advanced bioinformatics infrastructure for reliable and large-scale protein annotation and biological knowledge discovery. The Protein Information Resource (PIR) provides an integrated public resource of protein informatics to support genomic and proteomic research. PIR produces the Protein Sequence Database of functionally annotated protein sequences. The annotation problems are addressed by a classification-driven and rule-based method with evidence attribution, coupled with an integrated knowledge base system being developed. The approach allows sensitive identification, consistent and rich annotation, and systematic detection of annotation errors, as well as distinction of experimentally verified and computationally predicted features. The knowledge base consists of two new databases, sequence analysis tools, and graphical interfaces. PIR-NREF, a non-redundant reference database, provides a timely and comprehensive collection of all protein sequences, totaling more than 1,000,000 entries. iProClass, an integrated database of protein family, function, and structure information, provides extensive value-added features for about 830,000 proteins with rich links to over 50 molecular databases. This paper describes our approach to protein functional annotation with case studies and examines common identification errors. It also illustrates that data integration in PIR supports exploration of protein relationships and may reveal protein functional associations beyond sequence homology.
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 .
471313
Dependence network modeling for biomarker identification
MOTIVATION
Our purpose is to develop a statistical modeling approach for cancer biomarker discovery and provide new insights into early cancer detection. We propose the concept of dependence network, apply it for identifying cancer biomarkers, and study the difference between the protein or gene samples from cancer and non-cancer subjects based on mass-spectrometry (MS) and microarray data.


RESULTS
Three MS and two gene microarray datasets are studied. Clear differences are observed in the dependence networks for cancer and non-cancer samples. Protein/gene features are examined three at one time through an exhaustive search. Dependence networks are constructed by binding triples identified by the eigenvalue pattern of the dependence model, and are further compared to identify cancer biomarkers. Such dependence-network-based biomarkers show much greater consistency under 10-fold cross-validation than the classification-performance-based biomarkers. Furthermore, the biological relevance of the dependence-network-based biomarkers using microarray data is discussed. The proposed scheme is shown promising for cancer diagnosis and prediction.


AVAILABILITY
See supplements: http://dsplab.eng.umd.edu/~genomics/dependencenetwork/
5414394
Artificial Neural Networks for Molecular Sequence Analysis
Artificial neural networks provide a unique computing architecture whose potential has attracted interest from researchers across different disciplines. As a technique for computational analysis, neural network technology is very well suited for the analysis of molecular sequence data. It has been applied successfully to a variety of problems, ranging from gene identification, to protein structure prediction and sequence classification. This article provides an overview of major neural network paradigms, discusses design issues, and reviews current applications in DNA/RNA and protein sequence analysis.
21872273
The Protein Information Resource (PIR)
The Protein Information Resource (PIR) produces the largest, most comprehensive, annotated protein sequence database in the public domain, the PIR-International Protein Sequence Database, in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Sequence Database (JIPID). The expanded PIR WWW site allows sequence similarity and text searching of the Protein Sequence Database and auxiliary databases. Several new web-based search engines combine searches of sequence similarity and database annotation to facilitate the analysis and functional identification of proteins. New capabilities for searching the PIR sequence databases include annotation-sorted search, domain search, combined global and domain search, and interactive text searches. The PIR-International databases and search tools are accessible on the PIR WWW site at http://pir.georgetown.edu and at the MIPS WWW site at http://www. mips.biochem.mpg.de. The PIR-International Protein Sequence Database and other files are also available by FTP.
205225795
ProClass protein family database
ProClass is a protein family database that organizes non-redundant sequence entries into families defined collectively by PROSITE patterns and PIR superfamilies. By combining global similarities and functional motifs into a single classification scheme, ProClass helps to reveal domain and family relationships and classify multi-domain proteins. The database currently consists of more than 120 000 sequence entries, approximately 60% of which is classified into about 3500 families. To maximize family information retrieval, the database provides links to various protein family/domain and structural class databases and contains multiple motif alignments of all PROSITE patterns as well as global alignments of PIR superfamilies. The motif sequences are retrieved from both PIR-International and SWISS-PROT databases, including a large number of new members detected by our GeneFIND family identification system. ProClass can be used to support full-scale genomic annotation, because of its high classification rate. The ProClass database is available for on-line search and record retrieval from our WWW server at http://diana.uthct.edu/proclass.html
17356448
Web Directory Integration Using Conditional Random Fields
The purpose of integrating web directories is to transfer instances from a source to a target directory. Unlike conventional text categorization, in directory integration, there is extra information about the source directory that can be used to improve the classification accuracy. Many approaches exploit the measured similarity between two corresponding classes to enhance traditional text classifiers. These methods perform well if the topics of two classes are very similar, but they could lead to misclassification if the topics are dissimilar. We propose a directory integration approach based on the conditional random fields (CRFs) model, and model the integration process using a finite-state model. The advantage of using CRFs is that the transition features naturally include information about the relations between classes. Our results show that CRFs outperform conventional text classifiers. In addition, CRFs allow us to apply complex features to integrate the information about the contents of class and their labels. The performance of our approach can be improved by applying these features, especially for instances whose source and target classes are moderately similar
206622161
The Reverse-Exchange Interconnection Network
Properties of the reverse-exchange interconnection network are used to develop a reconfiguration scheme and a two-pass structure for enhancing the efficiency of a class of multistage interconnection networks. Functional relationships among a class of multistage interconnection networks are first derived. According to the functional relationships, we propose a reconfiguration scheme which enables a network to accomplish various interconnection functions of other networks. Then the admissible permutations along with related recursive control algorithms of the reverse-exchange interconnection network are specified through a set of theorems. Using the reverse-exchange property, we also prove that the algorithms actually work. Finally, we prove that arbitrary permutations can be realized in two passes (or 2 · 1og2N switching steps where N is the network size). By taking advantage of Benes network control algorithms, a way to control the two-pass structure is also developed.
1682394
Ontology-based Text Summarization for Business News Articles
In this paper, we compare two methods for article summarization. The first method is mainly based on term-frequency, while the second method is based on ontology. We build an ontology database for analyzing the main topics of the article. After identifying the main topics and determining their relative significance, we rank the paragraphs based on the relevance between main topics and each individual paragraph. Depending on the ranks, we choose desired proportion of paragraphs as summary. Experimental results indicate that both methods offer similar accuracy in their selections of the paragraphs.
26616615
On a Class of Multistage Interconnection Networks
A baseline network and a configuration concept are introduced to evaluate relationships among some proposed multistage interconnection networks. It is proven that the data manipulator (modified version), flip network, omega network, indirect binary n-cube network, and regular SW banyan network (S = F = 2) are topologically equivalent. The configuration concept facilitates developing a homogeneous routing algorithm which allows one-to-one and one- to-many connections from an arbitrary side of a network to the other side. This routing algorithm is extended to full communication which allows connections between terminals on the same side of a network. A conflict resolution scheme is also included. Some practical implications of our results are presented for further research.
15660415
On-the-fly sharing for streamed aggregation
Data streaming systems are becoming essential for monitoring applications such as financial analysis and network intrusion detection. These systems often have to process many similar but different queries over common data. Since executing each query separately can lead to significant scalability and performance problems, it is vital to share resources by exploiting similarities in the queries. In this paper we present ways to efficiently share streaming aggregate queries with differing periodic windows and arbitrary selection predicates. A major contribution is our sharing technique that does not require any up-front multiple query optimization. This is a significant departure from existing techniques that rely on complex static analyses of fixed query workloads. Our approach is particularly vital in streaming systems where queries can join and leave the system at any point. We present a detailed performance study that evaluates our strategies with an implementation and real data. In these experiments, our approach gives us as much as an order of magnitude performance improvement over the state of the art.