292216
Motif identification neural design for rapid and sensitive protein family search
A new method, the motif identification neural design (MOTIFIND), has been developed for rapid and sensitive protein family identification. The method is an extension of our previous gene classification artificial neural system and employs new designs to enhance the detection of distant relationships. The new designs include an n-gram term weighting algorithm for extracting local motif patterns, an enhanced n-gram method for extracting residues of long-range correlation, and integrated neural networks for combining global and motif sequence information. The system has been tested and compared with several existing methods using three protein families, the cytochrome c, cytochrome b and flavodoxin. Overall it achieves 100% sensitivity and > 99.6% specificity, an accuracy comparable to BLAST, but at a speed of approximately 20 times faster. The system is much more robust than the PROSITE search which is based on simple signature patterns. MOTIFIND also compares favorably with BLIMPS, the Hidden Markov Model and PROFILESEARCH in detecting fragmentary sequences lacking complete motif regions and in detecting distant relationships, especially for members of under-represented subgroups within a family. MOTIFIND may be generally applicable to other proteins and has the potential to become a full-scale database search and sequence analysis tool.
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.
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/
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.
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 .
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.
7582647
On self-similarity and hamiltonicity of dual-cubes
The dual-cube is a newly proposed topology for interconnection networks, which uses low dimensional hypercubes as building blocks. The primary advantages of the dual-cube over the hypercube are that, with the same node degree n, the dual-cube contains 2/sup n-1/ times more nodes than the hypercube and, with the same amount of nodes, the dual-cube has approximately 50% less links than the hypercube. This paper was focused on the investigations of the structural self-similarity and the Hamiltonian property of the dual-cube. It was shown that a dual-cube can be recursively constructed from lower dimensional dual-cubes and, conversely, a dual-cube can be recursively decomposed into lower dimensional dual-cubes. It was also proved that all dual-cubes are Hamiltonian. There exist multiple Hamiltonian cycles on a dual-cube, among which, [(n-1)/2] cycles are edge-disjoint. It was illustrated that rings and linear arrays can be effectively emulated on dual-cubes. Some strategies for track sharing in efficient VLSI layout design were also discussed.
7629632
Speech content authentication integrated with CELP speech decoders
A speech content authentication scheme, which is integrated with CELP speech coders to minimize the total computational cost is proposed in this research. Speech features relevant to semantic meaning are extracted, encrypted and attached as the header information. A low cost synchronization algorithm is used to resolve mis-synchronization caused by content preserving operations. Silent and tonal regions in the speech are identified with algorithms of low complexity to enhance the precision of integrity verification. This scheme is not only much faster than traditional cryptographic bitstream integrity algorithms, but also more compatible for a variety of applications. Experimental results are collected by using the GSM-AMR speech coder, and statistical analysis is performed to calculate the false positive rate of tamper detection.
29409365
A Parallel Asynchronous Garbage Collection Algorithm for Distributed Systems
The problem of distributed garbage collection is discussed. An algorithm for parallel distributed asynchronous garbage collection is presented. The liveness and safety properties of this method are demonstrated. The algorithm does not require a global clock, complex termination detection methods, or distributed synchronization techniques. A new color code is introduced to distinguish between local cells (black) and those that are exclusively accessible from the remote pointers (gray). The mutator operation is revised to handle a multiple mutator scheme on a given local memory. Simulation results show that the developed distributed and parallel algorithm performs much better than the sequential method as tested on a Balance 8000 computer. >
31789422
Performance Analysis of Multistage Interconnection Network Configurations and Operations
A performance evaluation using both analytical and simulation models, of circuit-switching multistage interconnection networks in aspects of configurations and operations is presented. Two configurations of the networks, single and dual, are evaluated. Network operations considered include conflict resolution strategies and communication strategies. Two different conflict resolution strategies, drop and hold, are analyzed. New analyses using Markov chains, are given, and are verified by simulation results. In the single-network configuration, it is shown that the drop strategy is better than the hold strategy for randomly distributed traffic. In the dual network configuration, five different communication strategies are investigated, and the optimum performance level is shown to be dependent on the length of the data transfer time. >
47400657
Construction of correlation immune Boolean functions
It is shown in this paper that every correlation immune Boolean function of n variables can be written as f(x) = g(xGT ), where g is an algebraic non-degenerate Boolean function of k (k ≤ n) variables and G is a generating matrix of an [n, k, d] linear code. It is known that the correlation immunity of f (x) is at least d − 1. In this paper we further prove when the correlation immunity exceeds this lower bound. A method which can theoretically search exhaustively all possible correlation immune functions is proposed, while constructions of higher order correlation immune functions as well as algebraic non-degenerate correlation immune functions are discussed in particular. It is also shown that many cryptographic properties of g can be inherited by the correlation immune function f (x) = g(xGT) which is an important property for choosing useful correlation immune functions.