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PubMed2003

The Drosophila melanogaster genome sequencing and annotation projects: a status report.

The sequence and genome annotations of Drosophila melanogaster were initially published in late 1999 and early 2000. Since then, the Berkeley Drosophila Genome Project (BDGP) and FlyBase have improved the quality of the sequence and reviewed the annotations by hand, respectively, to produce an account of the fruit fly genome that is of the highest quality. This review discusses the main features of this process, both from the point of view of the biology revealed in the end result and in the development of software that has been central to this genome sequencing and annotation project.

Animals↗

PubMed2000

TRES: comparative promoter sequence analysis.

Comparative promoter analysis is a promising strategy for elucidation of common regulatory modules conserved in evolutionarily related sequences or in genes showing common expression profiles. To facilitate such analysis, we have developed a software tool that detects conserved transcription factor binding sites, cis-elements, palindromes and k-tuples simultaneously in a set of sequences, and thus helps to identify putative motifs for designing further experiments.

Animals↗

PubMed2004

Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy.

MOTIVATION: Non-coding RNAs (ncRNAs)-functional RNA molecules not coding for proteins-are grouped into hundreds of families of homologs. To find new members of an ncRNA gene family in a large genome database, covariance models (CMs) are a useful statistical tool, as they use both sequence and RNA secondary structure information. Unfortunately, CM searches are slow. Previously, we introduced 'rigorous filters', which provably sacrifice none of CMs' accuracy, although often scanning much faster. A rigorous filter, using a profile hidden Markov model (HMM), is built based on the CM, and filters the genome database, eliminating sequences that provably could not be annotated as homologs. The CM is run only on the remainder. Some biologically important ncRNA families could not be scanned efficiently with this technique, largely due to the significance of conserved secondary structure relative to primary sequence in identifying these families. Current heuristic filters are also expected to perform poorly on such families. RESULTS: By augmenting profile HMMs with limited secondary structure information, we obtain rigorous filters that accelerate CM searches for virtually all known ncRNA families from the Rfam Database and tRNA models in tRNAscan-SE. These filters scan an 8 gigabase database in weeks instead of years, and uncover homologs missed by heuristic techniques to speed CM searches. AVAILABILITY: Software in development; contact the authors.

Algorithms↗

PubMed2004

SlidingBayes: exploring recombination using a sliding window approach based on Bayesian phylogenetic inference.

We developed a software tool (SlidingBayes) for recombination analysis based on Bayesian phylogenetic inference. Sliding-Bayes provides a powerful approach for detecting potential recombination, especially between highly divergent sequences and complex HIV-1 recombinants for which simpler methods like neighbor joining (NJ) may be less powerful. SlidingBayes guides Markov Chain Monte Carlo (MCMC) sampling performed by MrBayes in a sliding window across the alignment (Bayesian scanning). The tool can be used for nucleotide and amino acid sequences and combines all the modeling possibilities of MrBayes with the ability to plot the posterior probability support for clustering of various combinations of taxa.

Algorithms↗

PubMed2005

A grid layout algorithm for automatic drawing of biochemical networks.

MOTIVATION: Visualization is indispensable in the research of complex biochemical networks. Available graph layout algorithms are not adequate for satisfactorily drawing such networks. New methods are required to visualize automatically the topological architectures and facilitate the understanding of the functions of the networks. RESULTS: We propose a novel layout algorithm to draw complex biochemical networks. A network is modeled as a system of interacting nodes on squared grids. A discrete cost function between each node pair is designed based on the topological relation and the geometric positions of the two nodes. The layouts are produced by minimizing the total cost. We design a fast algorithm to minimize the discrete cost function, by which candidate layouts can be produced efficiently. A simulated annealing procedure is used to choose better candidates. Our algorithm demonstrates its ability to exhibit cluster structures clearly in relatively compact layout areas without any prior knowledge. We developed Windows software to implement the algorithm for CADLIVE. AVAILABILITY: All materials can be freely downloaded from http://kurata21.bio.kyutech.ac.jp/grid/grid_layout.htm; http://www.cadlive.jp/ SUPPLEMENTARY INFORMATION: http://kurata21.bio.kyutech.ac.jp/grid/grid_layout.htm; http://www.cadlive.jp/

Algorithms↗

PubMed2005

Bioinformatic analysis of exon repetition, exon scrambling and trans-splicing in humans.

MOTIVATION: Using bioinformatic approaches we aimed to characterize poorly understood abnormalities in splicing known as exon scrambling, exon repetition and trans-splicing. RESULTS: We developed a software package that allows large-scale comparison of all human expressed sequence tags (EST) sequences to the entire set of human gene sequences. Among 5,992,495 EST sequences, 401 cases of exon repetition and 416 cases of exon scrambling were found. The vast majority of identified ESTs contain fragments rather than full-length repeated or scrambled exons. Their structures suggest that the scrambled or repeated exon fragments may have arisen in the process of cDNA cloning and not from splicing abnormalities. Nevertheless, we found 11 cases of full-length exon repetition showing that this phenomenon is real yet very rare. In searching for examples of trans-splicing, we looked only at reproducible events where at least two independent ESTs represent the same putative trans-splicing event. We found 15 ESTs representing five types of putative trans-splicing. However, all 15 cases were derived from human malignant tissues and could have resulted from genomic rearrangements. Our results provide support for a very rare but physiological occurrence of exon repetition, but suggest that apparent exon scrambling and trans-splicing result, respectively, from in vitro artifact and gene-level abnormalities. AVAILABILITY: Exon-Intron Database (EID) is available at http://www.meduohio.edu/bioinfo/eid. Programs are available at http://www.meduohio.edu/bioinfo/software.html. The Laboratory website is available at http://www.meduohio.edu/medicine/fedorov SUPPLEMENTARY INFORMATION: Supplementary file is available at http://www.meduohio.edu/bioinfo/software.html.

Algorithms↗

PubMed2006

Analysis assistant for single-molecule force spectroscopy data on membrane proteins--MPTV.

UNLABELLED: Force-distance (F-D) curves of single membrane proteins reveal information on inter- and intramolecular interactions occurring within a protein and between proteins. However, the analysis of single-molecule force spectroscopy data is a time consuming and complex process requiring objective criteria. In most cases the user requires additional information to interpret F-D curves. Therefore we developed a software assistant representing the force or molecular interaction pattern and the topology or the 3D structure of the membrane protein. This representation establishes a basis for detailed interpretation of the protein structure and its underlying molecular interactions. Various integrated bioinformatic features further assist in the interpretation of measured and assigned molecular interactions that determine membrane protein folding, structure, stability and function. Web queries and programs about the topology are directly linked. Motifs, helix types, representation of Venn diagrams and the complete functionality of the program Jmol belong to it. AVAILABILITY: The program MPTV is freely available from the website at http://www.bioforscher.de/mptv.htm/.

Algorithms↗

PubMed1997

RAGA: RNA sequence alignment by genetic algorithm.

We describe a new approach for accurately aligning two homologous RNA sequences when the secondary structure of one of them is known. To do so we developed two software packages, called RAGA and PRAGA, which use a genetic algorithm approach to optimize the alignments. RAGA is mainly an extension of SAGA, an earlier package for multiple protein sequence alignment. In PRAGA several genetic algorithms run in parallel and exchange individual solutions. This method allows us to optimize an objective function that describes the quality of a RNA pairwise alignment, taking into account both primary and secondary structure, including pseudoknots. We report results obtained using PRAGA on nine test cases of pairs of eukaryotic small subunit rRNA sequence (nuclear and mitochondrial).

Algorithms↗

PubMed1999

DNA Data Bank of Japan dealing with large-scale data submission.

The DNA Data Bank of Japan (DDBJ) (http//:www.ddbj.nig.ac.jp) has developed a software system for mass submissions to cope with a recent expansion of EST and genome data submissions. The system is composed of four parts, the WWW data submission, large-scale submission, submission management and storing. Using this system one can submit data on a large number of sequences or a very long sequence while checking the consistency between the annotation and sequence without much effort. DDBJ has received large scale data of Homo sapiens, Arabidopsis and Pyrococcus from Japanese researchers who made full use of the new submission system.

Animals↗

PubMed2002

Ordered catenation of sequence-tagged sites and multiplexed SNP genotyping by sequencing.

We describe a method for the efficient genotyping of SNPs, involving sequencing of ordered and catenated sequence-tagged sites (OCS). In OCS, short genomic segments, each containing an SNP, are amplified by PCR using primers that carry specially designed extra nucleotides at their 5'-ends. Amplification products are then combined and converted to a concatamer in a defined order by a second round of thermal cycling. The concatenation takes place because the 5'-ends of each amplicon are designed to be complementary to the ends of the presumptive neighboring amplicons. The primer sequences for OCS are chosen using newly developed dedicated software, OCS Optimizer. Using sets of SNPs, we show that at least 10 STSs can be concatenated in a predefined order and all SNPs in the STSs are accurately genotyped by one two-way sequencing reaction.

Asian People↗

PubMed2003

CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle.

The further understanding of the mechanisms of gene regulatory networks requires comprehensive tools for both the representation of complicated signal transduction pathways and the in silico identification of genomic signals that govern the regulation of gene expression. Consequently, sophisticated notation must be developed to represent the signal transduction pathways in a form that can be readily processed by both computers and humans. We propose the regulator-reaction equations combined with detailed attributes including the associated cellular component, molecular function, and biological process and present the simulation-directed graphical notation that is derived from modification of Kohn's method. We have developed the software suite, CADLIVE (Computer-Aided Design of LIVing systEms), which features a graphical user interface (GUI) to edit large-scale maps of complicated signal transduction pathways using a conventional XML-based representation. The regulator-reaction equations represent not only mechanistic reactions, but also semantic models containing ambiguous and incomplete processes. In order to demonstrate the feasibility of CADLIVE, we constructed a detailed map of the budding yeast cell cycle, which consists of 184 molecules and 152 reactions, in a really compact space. CADLIVE enables one to look at the whole view of a large-scale map, to integrate postgenomic data into the map, and to computationally simulate the signal transduction pathways, which greatly facilitates exploring novel or unexpected interactions.

Cell Cycle↗

PubMed2004

New strategy for the representation and the integration of biomolecular knowledge at a cellular scale.

The combination of sequencing and post-sequencing experimental approaches produces huge collections of data that are highly heterogeneous both in structure and in semantics. We propose a new strategy for the integration of such data. This strategy uses structured sets of sequences as a unified representation of biological information and defines a probabilistic measure of similarity between the sets. Sets can be composed of sequences that are known to have a biological relationship (e.g. proteins involved in a complex or a pathway) or that share similar values for a particular attribute (e.g. expression profile). We have developed a software, BlastSets, which implements this strategy. It exploits a database where the sets derived from diverse biological information can be deposited using a standard XML format. For a given query set, BlastSets returns target sets found in the database whose similarity to the query is statistically significant. The tool allowed us to automatically identify verified relationships between correlated expression profiles and biological pathways using publicly available data for Saccharomyces cerevisiae. It was also used to retrieve the members of a complex (ribosome) based on the mining of expression profiles. These first results validate the relevance of the strategy and demonstrate the promising potential of BlastSets.

Computational Biology↗

PubMed2004

The interactome as a tree--an attempt to visualize the protein-protein interaction network in yeast.

The refinement and high-throughput of protein interaction detection methods offer us a protein-protein interaction network in yeast. The challenge coming along with the network is to find better ways to make it accessible for biological investigation. Visualization would be helpful for extraction of meaningful biological information from the network. However, traditional ways of visualizing the network are unsuitable because of the large number of proteins. Here, we provide a simple but information-rich approach for visualization which integrates topological and biological information. In our method, the topological information such as quasi-cliques or spoke-like modules of the network is extracted into a clustering tree, where biological information spanning from protein functional annotation to expression profile correlations can be annotated onto the representation of it. We have developed a software named PINC based on our approach. Compared with previous clustering methods, our clustering method ADJW performs well both in retaining a meaningful image of the protein interaction network as well as in enriching the image with biological information, therefore is more suitable in visualization of the network.

Algorithms↗

PubMed2005

Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation.

The oligonucleotide specificity for microarray hybridization can be predicted by its sequence identity to non-targets, continuous stretch to non-targets, and/or binding free energy to non-targets. Most currently available programs only use one or two of these criteria, which may choose 'false' specific oligonucleotides or miss 'true' optimal probes in a considerable proportion. We have developed a software tool, called CommOligo using new algorithms and all three criteria for selection of optimal oligonucleotide probes. A series of filters, including sequence identity, free energy, continuous stretch, GC content, self-annealing, distance to the 3'-untranslated region (3'-UTR) and melting temperature (T(m)), are used to check each possible oligonucleotide. A sequence identity is calculated based on gapped global alignments. A traversal algorithm is used to generate alignments for free energy calculation. The optimal T(m) interval is determined based on probe candidates that have passed all other filters. Final probes are picked using a combination of user-configurable piece-wise linear functions and an iterative process. The thresholds for identity, stretch and free energy filters are automatically determined from experimental data by an accessory software tool, CommOligo_PE (CommOligo Parameter Estimator). The program was used to design probes for both whole-genome and highly homologous sequence data. CommOligo and CommOligo_PE are freely available to academic users upon request.

Algorithms↗

PubMed2001

Development of a multipurpose feed enzyme analyzer to estimate and evaluate the profitability of using feed enzyme preparations for poultry.

Previous studies have demonstrated that a log-linear equation could accurately predict chick performance when a feed enzyme was added to a diet and that the slope of the equation provided a measure of the efficacy of different enzymes. The objective of the study was to develop a software package, a Multipurpose Feed Enzyme Analyzer (MPFEA), based on an equation designed to evaluate the profitability of using feed enzymes. A high correlation between the efficacy of different feed enzymes (B values, the slopes of the equations) and the maximal profits was obtained when feed enzymes were added to a barley-based diet (r2 = 0.99, P < 0.0005). In contrast, there was a low correlation between the B values and the maximal profits when a feed enzyme was added to different cereal-based diets (r2 = 0.61, P = 0.2171). It appeared that there is not always a close association between efficacy of an enzyme when added to different cereal-based diets and the corresponding profitability. The MPFEA was highly versatile, as any combination of inputs such as the amounts of a feed enzyme and a substituted cereal required to yield a profit level could be determined. In conclusion, the MPFEA can accurately evaluate profitability of using different feed enzymes; select the most profitable cereal for a given feed enzyme; determine the optimal amounts of a feed enzyme, a cereal, or both; and even estimate the alternate price for a feed enzyme and a cereal. It should provide a useful tool for nutritionists.

Animal Feed↗

PubMed2001

Practical issues in bispectral analysis of electroencephalographic signals.

IMPLICATIONS: The aim of this report was to confirm the methodology of bispectral analysis of electroencephalogram. In developing a software for real-time bispectral analysis, we encountered several practical problems in bispectrum calculation. We settled those and concluded that 3 min of monitoring are required to obtain reliable and reproducible bicoherence values.

Algorithms↗

PubMed2002

Changes of electroencephalographic bicoherence during isoflurane anesthesia combined with epidural anesthesia.

BACKGROUND: The authors previously reported that, during isoflurane anesthesia, electroencephalographic bicoherence values changed in a fairly restricted region of frequency versus frequency space. The aim of the current study was to clarify the relation between electroencephalographic bicoherence and the isoflurane concentration. METHODS: Thirty elective abdominal surgery patients (male and female, aged 34-77 yr, American Society of Anesthesiologists physical status I-II) were enrolled. After electroencephalogram recording with patients in an awake state, anesthesia was induced with 3 mg/kg thiopental and maintained with oxygen and isoflurane. Continuous epidural anesthesia with 80-100 mg/kg 1% lidocaine was also administered. Using software they developed, the authors continuously recorded the FP1-A1 lead of the electroencephalographic signal and expired isoflurane concentration to an IBM-PC compatible computer. After confirming the steady state of each isoflurane (end-tidal concentration at 0.3, 0.5, 0.7, 0.9, 1.1, 1.3, and 1.5%), electroencephalographic bicoherence values were calculated. RESULTS: In a light anesthetic state, electroencephalographic bicoherence values were low (generally < or = 15.0%). At increased concentrations of isoflurane, two peaks of electroencephalographic bicoherence emerged along the diagonal line (f1=f2). The peak emerged at around 4.0 Hz and grew higher as isoflurane concentration increased until it reached a plateau (43.8 +/- 3.5%, mean +/- SD) at isoflurane 0.9%. The other peak, at about 10.0 Hz, also became significantly higher and reached a plateau (32.6 +/- 9.2%) at isoflurane 0.9%; at isoflurane 1.3%, however, this peak slightly decreased. CONCLUSION: Changes in the height of two electroencephalographic bicoherence peaks correlated well with isoflurane concentration.

Adult↗

PubMed1995

Anatomy of the clinical simulation.

Computer-based clinical simulations have been used in medical education for the past 25 years. During this period, the technology has evolved from mainframe computers to microcomputers to multimedia. All designers of simulations must decide which elements of reality to include explicitly in a simulated case, which to leave to the user's imagination, and when to intervene for educational purposes. Once these decisions are made, developers of simulations have many options for structuring the simulation itself. They can develop simulations with single or multiple patient encounters, with menu or natural-language requests for data, with varying levels of volunteered information about the simulated patient, with interpreted or uninterpreted clinical findings, with deterministic or probablistic evolution of the case, with various ways to give users feedback about their progress through the case, and with manual or automated creation of specific cases. Simulations derive their specific character from how these options are implemented.

Computer Simulation↗