Comparison of Bioelectrical Impedance Vector Analysis (BIVA) to 7-point Subjective Global Assessment for the diagnosis of malnutrition / Comparação da Análise Vetorial de Impedância Bioelétrica (BIVA) com a Avaliação Subjetiva Global de 7 pontos para o diagnóstico de desnutrição

Abstract Introduction: Bioelectrical impedance vector analysis (BIVA) is a non-invasive and low-cost strategy. The methods used to assess malnutrition in patients undergoing HD are still a challenge. The aim of the present study was to compare BIVA to 7-Point Subjective Global Assessment (7-point SGA) to identify malnutrition. We also investigated the sensitivity and specificity of the previously proposed cutoffs point for BIVA parameters. Methods: Patients of both sexes, over 20 years of age, on HD treatment were included. Anthropometric parameters, laboratory data, and bioelectrical impedance analysis (BIA) were evaluated. Values of resistance (R) and reactance (Xc) obtained by mono-frequency BIA were normalized to body height (H) to generate a graph of the bioimpedance vector with the BIVA software. The analysis of the area under the receiver operating curve ROC (AUC) was performed. Results: Among the included 104 patients, the mean age was 51.70 (±15.10) years, and 52% were male. The BIVA had a sensitivity of 35% for diagnosing malnutrition. The specificity of BIVA for identifying the well-nourished patients was 85.7%. The diagnostic accuracy between the BIVA and 7-point SGA was AUC=0.604; 95%CI 0.490-0.726, higher than the previously established cutoff values (AUC=0.514; 95%CI: 0.369-0.631). The 95% confidence ellipses did not overlap (p<0.05). Conclusion: Our study showed low accuracy of BIVA for diagnosing malnutrition using a 7-point SGA as a reference standard. However, it is a complementary method for assessing nutritional status as it provides data on cellularity and hydration, which are important aspects for the HD population.

Resumo Introdução: Análise vetorial de impedância bioelétrica (BIVA) é uma estratégia não invasiva e de baixo custo. Os métodos usados para avaliar desnutrição em pacientes em HD ainda são um desafio. O objetivo do presente estudo foi comparar BIVA com Avaliação Subjetiva Global de 7 pontos (ASG de 7 pontos) para identificar desnutrição. Também investigamos sensibilidade e especificidade do ponto de corte proposto anteriormente para parâmetros de BIVA. Métodos: Foram incluídos pacientes de ambos os sexos, acima de 20 anos, em HD. Foram avaliados parâmetros antropométricos, dados laboratoriais e análise de impedância bioelétrica (BIA). Valores de resistência (R) e reatância (Xc) obtidos por BIA de mono-frequência foram normalizados para altura corporal (H) gerando um gráfico do vetor de bioimpedância com a ajuda do software BIVA. Foi realizada uma análise da área sob a curva ROC (AUC). Resultados: Entre 104 pacientes incluídos, a idade média foi 51,70 (±15,10) anos, e 52% eram homens. BIVA demonstrou sensibilidade de 35% para diagnosticar desnutrição. A especificidade da BIVA para identificar pacientes bem nutridos foi 85,7%. A precisão diagnóstica entre BIVA e ASG de 7 pontos foi AUC=0,604; IC95%: 0,490-0,726, superior aos valores de corte estabelecidos anteriormente (AUC=0,514; IC95%: 0,369-0,631). Elipses de confiança de 95% não se sobrepuseram (p<0,05). Conclusão: Nosso estudo mostrou baixa precisão da BIVA para diagnóstico de desnutrição usando ASG-7 pontos como padrão de referência. Entretanto, é um método complementar para avaliar estado nutricional, pois fornece dados sobre celularidade e hidratação, aspectos importantes para a população em HD.

Comparison of Bioelectrical Impedance Vector Analysis (BIVA) to 7-point Subjective Global Assessment for the diagnosis of malnutrition.

INTRODUCTION: Bioelectrical impedance vector analysis (BIVA) is a non-invasive and low-cost strategy. The methods used to assess malnutrition in patients undergoing HD are still a challenge. The aim of the present study was to compare BIVA to 7-Point Subjective Global Assessment (7-point SGA) to identify malnutrition. We also investigated the sensitivity and specificity of the previously proposed cutoffs point for BIVA parameters. METHODS: Patients of both sexes, over 20 years of age, on HD treatment were included. Anthropometric parameters, laboratory data, and bioelectrical impedance analysis (BIA) were evaluated. Values of resistance (R) and reactance (Xc) obtained by mono-frequency BIA were normalized to body height (H) to generate a graph of the bioimpedance vector with the BIVA software. The analysis of the area under the receiver operating curve ROC (AUC) was performed. RESULTS: Among the included 104 patients, the mean age was 51.70 (±15.10) years, and 52% were male. The BIVA had a sensitivity of 35% for diagnosing malnutrition. The specificity of BIVA for identifying the well-nourished patients was 85.7%. The diagnostic accuracy between the BIVA and 7-point SGA was AUC=0.604; 95%CI 0.490-0.726, higher than the previously established cutoff values (AUC=0.514; 95%CI: 0.369-0.631). The 95% confidence ellipses did not overlap (p<0.05). CONCLUSION: Our study showed low accuracy of BIVA for diagnosing malnutrition using a 7-point SGA as a reference standard. However, it is a complementary method for assessing nutritional status as it provides data on cellularity and hydration, which are important aspects for the HD population.

The relationship between grip strength with health-related quality of life and mortality in hemodialysis patients.

Purpose: Hemodialysis (HD) is a therapeutic modality that enables the highest survival for individuals with chronic kidney disease (CKD). In contrast, HD contributes to the pro-inflammatory state and may negatively affect the muscle strength and quality of life (QoL) of these individuals. To date, few studies have evaluated the association between decrease in strength and QoL in HD patients. Thus, our objective was to assess whether diminished muscle strength is associated with worse health related QoL and mortality. Methods: We included patients aged ≥ 18 years on HD. Clinical and demographic data were collected from patients' medical records. Clinical data, nutritional status (laboratory, anthropometry, bioimpedance analysis) and health-related QoL (World Health Organization's quality of life questionnaire, WHOQOL-Bref) were analyzed at baseline. Mortality was recorded for 32 months. Results: Among the 105 patients evaluated, the median age was 52 (43-64) years, and males were predominant (n = 73; 70%). The general median of QoL was 66.8 ± 11.9. Approximately 30% of patients were considered to have a worse QoL and 12,4% to have low muscle strength. This was not associated with QoL and mortality. HD vintage greater then to 5 years was associated with higher dissatisfaction in the perception of the environmental domain and overall QoL. Conclusion: Our data suggest that low muscle strength was not associated with health-related QoL using the WHOQOL-Bref instrument and mortality.

Short-Term Creatine Supplementation May Alleviate the Malnutrition-Inflammation Score and Lean Body Mass Loss in Hemodialysis Patients: A Pilot Randomized Placebo-Controlled Trial.

BACKGROUND: Creatine supplementation has been proposed to alleviate muscle loss in various populations, but has not been investigated in hemodialysis (HD) patients. Thus, our objective was to evaluate whether creatine supplementation could attenuate the loss of lean body mass (LBM) and malnutrition-inflammation score (MIS) in HD patients. METHODS: A randomized, placebo-controlled, double blind, parallel-design study included HD patients, of both sexes, aged 18-59 years. The patients were allocated to a Placebo Group (PG; n = 15; received maltodextrin, 1st week: 40 g/day and 2nd-4th weeks: 10 g/day) and a Creatine Group (CG; n = 15; received creatine plus maltodextrin, 1st week: 20 g/day of creatine plus 20 g/day of maltodextrin and 2nd-4th weeks: 5 g/day of creatine plus 5 g/day of maltodextrin). Pre and post the intervention, patients were evaluated for food intake, MIS, body composition and biochemical parameters. RESULTS: CG group attenuated the MIS (Pre: 5.57 ± 0.72 vs. Post: 3.85 ± 0.47 score, P = 0.003) compared with PG (Pre: 5.71 ± 0.97 vs. Post: 5.36 ± 0.95 score, P = 0.317) (supplement × time P = 0.017, effect size: 0.964). The change of LBM was greater in CG than in PG (CG: Δ0.95 vs PG: Δ0.13 kg). At post-intervention, 28.6% of PG patients presented LBM loss and 71.4% remain stable. In contrast, 14.4% of CG patients had LBM loss, 42.8% remain stable and 42.8% gained. Food intake and quality of life did not change. CG increased the BMI and gait speed in post-compared to pre-moment, but no difference among the groups. CONCLUSION: In HD patients, four weeks of creatine supplementation may alleviate the MIS as well as attenuate the LBM loss compared to placebo.

Total protein or leucine intakes are not associated with handgrip strength in hemodialysis patients: A pilot study.

BACKGROUND & AIMS: Inadequate protein intake is associated with lean body mass (LBM) loss. However, it is unclear whether high protein diet and leucine intake are associated with handgrip strength (HGS), a validated marker of muscle function. This study aims to: i) assess the prevalence of patients with low HGS; and ii) verify if HGS is correlated with high protein diet and leucine consumption in hemodialysis patients. METHODS: This cross-sectional study analysed patients at two center hemodialysis (HD) clinic and sixty-two patients aged ∼39 years with length of time on HD ∼60 months undergoing HD was carried out. Body weight (kg), LBM (kg) and body fat mass (%) assessments were performed by dual-energy X-ray absorptiometry and height (m) through portable stadiometer. Body mass index (BMI) (kg/m2) was calculated using the body weight and height. HGS (kg) was measured using a hydraulic dynamometer. Fisher's exact test, Chi-square, Pearson's correlation, and logistic regression were done to test the hypothesis. RESULTS: Out of 62 patients, 47 (75.8%) presented low HGS. In addition, no correlation was found between protein intake (if in percentage or g/kg/d) and HGS (r = 0.07, p = 0.58; r = -0.04, p = 0.70, respectively). Although there is a low correlation among leucine intake (g/d) and HGS (r = 0.39, p = 0.01), low HGS was not associated with leucine intake in the crude model (OR: 0.86 95%CI(0.60-1.24) p = 0.441), nor after adjustment for age, sex and BMI (OR: 0.84 95%CI(0.56-1.26), p = 0.422). CONCLUSIONS: Approximately 75% of patients undergoing hemodialysis presented low HGS. Additionally, neither a high protein diet nor leucine intake was associated with the HGS values.

Pre-sarcopenia in patients undergoing hemodialysis: Prevalence and association with biochemical parameters.

BACKGROUND & AIMS: Albumin and C reactive protein (CRP) concentrations are associated with the loss of lean body mass in the elderly. However, it remains to be ascertained whether these parameters are associated with pre-sarcopenia of chronic renal failure adult's patients undergoing replacement therapy. Therefore, we aimed to investigate the prevalence of pre-sarcopenia and it association with serum albumin and CRP concentrations in adult patients. METHODS: A cross-sectional study was conducted enrolling hemodialysis patients. Body weight, body mass index (BMI), and arm, thigh and calf circumferences were assessed using the inelastic tape; handgrip strength using a dynamometer; and body fat mass and appendicular lean mass (ALM) using the DXA. The classification of pre-sarcopenia was obtained by ALM values. RESULTS: From sixty-two patients, 35.5% were diagnosed with pre-sarcopenia. Logistic regression analysis revealed no show association between pre-sarcopenia (absence or presence) with serum CRP or albumin concentrations in both models, crude or adjusted by body fat mass. CONCLUSIONS: Approximately one-third of patients undergoing replacement therapy presented pre-sarcopenia, but no association with serum albumin and CRP concentrations were found.

The semantic web in translational medicine: current applications and future directions.

Semantic web technologies offer an approach to data integration and sharing, even for resources developed independently or broadly distributed across the web. This approach is particularly suitable for scientific domains that profit from large amounts of data that reside in the public domain and that have to be exploited in combination. Translational medicine is such a domain, which in addition has to integrate private data from the clinical domain with proprietary data from the pharmaceutical domain. In this survey, we present the results of our analysis of translational medicine solutions that follow a semantic web approach. We assessed these solutions in terms of their target medical use case; the resources covered to achieve their objectives; and their use of existing semantic web resources for the purposes of data sharing, data interoperability and knowledge discovery. The semantic web technologies seem to fulfill their role in facilitating the integration and exploration of data from disparate sources, but it is also clear that simply using them is not enough. It is fundamental to reuse resources, to define mappings between resources, to share data and knowledge. All these aspects allow the instantiation of translational medicine at the semantic web-scale, thus resulting in a network of solutions that can share resources for a faster transfer of new scientific results into the clinical practice. The envisioned network of translational medicine solutions is on its way, but it still requires resolving the challenges of sharing protected data and of integrating semantic-driven technologies into the clinical practice.

slaMEM: efficient retrieval of maximal exact matches using a sampled LCP array.

MOTIVATION: Maximal exact matches, or just MEMs, are a powerful tool in the context of multiple sequence alignment and approximate string matching. The most efficient algorithms to collect them are based on compressed indexes that rely on longest common prefix array-centered data structures. However, their space-efficient representations make use of encoding techniques that are expensive from a computational point of view. With the deluge of data generated by high-throughput sequencing, new approaches need to be developed to deal with larger genomic sequences. RESULTS: In this work, we have developed a new longest common prefix array-sampled representation, optimized to work with the backward search method inherently used by the FM-Index. Unlike previous implementations that sacrifice running time to have smaller space, ours lead to both a fast and a space-efficient approach. This implementation was used by the new software slaMEM, developed to efficiently retrieve MEMs. The results show that the new algorithm is competitive against existing state-of-the-art approaches. AVAILABILITY AND IMPLEMENTATION: The software is implemented in C and is operating system independent. The source code is freely available for download at http://github.com/fjdf/slaMEM/ under the GPLv3 license.

Enrichment analysis applied to disease prognosis.

: Enrichment analysis is well established in the field of transcriptomics, where it is used to identify relevant biological features that characterize a set of genes obtained in an experiment.This article proposes the application of enrichment analysis as a first step in a disease prognosis methodology, in particular of diseases with a strong genetic component. With this analysis the objective is to identify clinical and biological features that characterize groups of patients with a common disease, and that can be used to distinguish between groups of patients associated with disease-related events. Data mining methodologies can then be used to exploit those features, and assist medical doctors in the evaluation of the patients in respect to their predisposition for a specific event.In this work the disease hypertrophic cardiomyopathy (HCM) is used as a case-study, as a first test to assess the feasibility of the application of an enrichment analysis to disease prognosis. To perform this assessment, two groups of patients have been considered: patients that have suffered a sudden cardiac death episode and patients that have not.The results presented were obtained with genetic data and the Gene Ontology, in two enrichment analyses: an enrichment profiling aiming at characterizing a group of patients (e.g. that suffered a disease-related event) based on their mutations; and a differential enrichment aiming at identifying differentiating features between a sub-group of patients and all the patients with the disease. These analyses correspond to an adaptation of the standard enrichment analysis, since multiple sets of genes are being considered, one for each patient.The preliminary results are promising, as the sets of terms obtained reflect the current knowledge about the gene functions commonly altered in HCM patients, thus allowing their characterization. Nevertheless, some factors need to be taken into consideration before the full potential of the enrichment analysis in the prognosis methodology can be evaluated. One of such factors is the need to test the enrichment analysis with clinical data, in addition to genetic data, since both types of data are expected to be necessary for prognosis purposes.

Empirical assessment of sequencing errors for high throughput pyrosequencing data.

BACKGROUND: Sequencing-by-synthesis technologies significantly improve over the Sanger method in terms of speed and cost per base. However, they still usually fail to compete in terms of read length and quality. Current high-throughput implementations of the pyrosequencing technique yield reads whose length approach those of the capillary electrophoresis method. A less obvious question is whether their quality is affected by platform-specific sequencing errors. RESULTS: We present an empirical study aimed at assessing the quality and characterising sequencing errors for high throughput pyrosequencing data. We have developed a procedure for extracting sequencing error data from genome assemblies and study their characteristics, in particular the length distribution of indel gaps and their relation to the sequence contexts where they occur. We used this procedure to analyse data from three prokaryotic genomes sequenced with the GS FLX technology. We also compared two models previously employed with success for peptide sequence alignment. CONCLUSIONS: We observed an overall very low error rate in the analysed data, with indel errors being much more abundant than substitutions. We also observed a dependence between the length of the gaps and that of the homopolymer context where they occur. As with protein alignments, a power-law model seems to approximate the indel errors more accurately, although the results are not so conclusive as to justify a depart from the commonly used affine gap penalty scheme. In whichever case, however, our procedure can be used to estimate more realistic error model parameters.

Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches.

MOTIVATION: The computational search for novel microRNA (miRNA) precursors often involves some sort of structural analysis with the aim of identifying which type of structures are prone to being recognized and processed by the cellular miRNA-maturation machinery. A natural way to tackle this problem is to perform clustering over the candidate structures along with known miRNA precursor structures. Mixed clusters allow then the identification of candidates that are similar to known precursors. Given the large number of pre-miRNA candidates that can be identified in single-genome approaches, even after applying several filters for precursor robustness and stability, a conventional structural clustering approach is unfeasible. RESULTS: We propose a method to represent candidate structures in a feature space, which summarizes key sequence/structure characteristics of each candidate. We demonstrate that proximity in this feature space is related to sequence/structure similarity, and we select candidates that have a high similarity to known precursors. Additional filtering steps are then applied to further reduce the number of candidates to those with greater transcriptional potential. Our method is compared with another single-genome method (TripletSVM) in two datasets, showing better performance in one and comparable performance in the other, for larger training sets. Additionally, we show that our approach allows for a better interpretation of the results. AVAILABILITY AND IMPLEMENTATION: The MinDist method is implemented using Perl scripts and is freely available at http://www.cravela.org/?mindist=1. CONTACT: backofen@informatik.uni-freiburg.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Quantitative modeling of the Saccharomyces cerevisiae FLR1 regulatory network using an S-system formalism.

In this study we address the problem of finding a quantitative mathematical model for the genetic network regulating the stress response of the yeast Saccharomyces cerevisiae to the agricultural fungicide mancozeb. An S-system formalism was used to model the interactions of a five-gene network encoding four transcription factors (Yap1, Yrr1, Rpn4 and Pdr3) regulating the transcriptional activation of the FLR1 gene. Parameter estimation was accomplished by decoupling the resulting system of nonlinear ordinary differential equations into a larger nonlinear algebraic system, and using the Levenberg-Marquardt algorithm to fit the models predictions to experimental data. The introduction of constraints in the model, related to the putative topology of the network, was explored. The results show that forcing the network connectivity to adhere to this topology did not lead to better results than the ones obtained using an unrestricted network topology. Overall, the modeling approach obtained partial success when trained on the nonmutant datasets, although further work is required if one wishes to obtain more accurate prediction of the time courses.

Efficient alignment of pyrosequencing reads for re-sequencing applications.

BACKGROUND: Over the past few years, new massively parallel DNA sequencing technologies have emerged. These platforms generate massive amounts of data per run, greatly reducing the cost of DNA sequencing. However, these techniques also raise important computational difficulties mostly due to the huge volume of data produced, but also because of some of their specific characteristics such as read length and sequencing errors. Among the most critical problems is that of efficiently and accurately mapping reads to a reference genome in the context of re-sequencing projects. RESULTS: We present an efficient method for the local alignment of pyrosequencing reads produced by the GS FLX (454) system against a reference sequence. Our approach explores the characteristics of the data in these re-sequencing applications and uses state of the art indexing techniques combined with a flexible seed-based approach, leading to a fast and accurate algorithm which needs very little user parameterization. An evaluation performed using real and simulated data shows that our proposed method outperforms a number of mainstream tools on the quantity and quality of successful alignments, as well as on the execution time. CONCLUSIONS: The proposed methodology was implemented in a software tool called TAPyR--Tool for the Alignment of Pyrosequencing Reads--which is publicly available from http://www.tapyr.net.

Advancing Eucalyptus genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries.

BACKGROUND: Eucalyptus species are among the most planted hardwoods in the world because of their rapid growth, adaptability and valuable wood properties. The development and integration of genomic resources into breeding practice will be increasingly important in the decades to come. Bacterial artificial chromosome (BAC) libraries are key genomic tools that enable positional cloning of important traits, synteny evaluation, and the development of genome framework physical maps for genetic linkage and genome sequencing. RESULTS: We describe the construction and characterization of two deep-coverage BAC libraries EG_Ba and EG_Bb obtained from nuclear DNA fragments of E. grandis (clone BRASUZ1) digested with HindIII and BstYI, respectively. Genome coverages of 17 and 15 haploid genome equivalents were estimated for EG_Ba and EG_Bb, respectively. Both libraries contained large inserts, with average sizes ranging from 135 Kb (Eg_Bb) to 157 Kb (Eg_Ba), very low extra-nuclear genome contamination providing a probability of finding a single copy gene ≥ 99.99%. Libraries were screened for the presence of several genes of interest via hybridizations to high-density BAC filters followed by PCR validation. Five selected BAC clones were sequenced and assembled using the Roche GS FLX technology providing the whole sequence of the E. grandis chloroplast genome, and complete genomic sequences of important lignin biosynthesis genes. CONCLUSIONS: The two E. grandis BAC libraries described in this study represent an important milestone for the advancement of Eucalyptus genomics and forest tree research. These BAC resources have a highly redundant genome coverage (> 15×), contain large average inserts and have a very low percentage of clones with organellar DNA or empty vectors. These publicly available BAC libraries are thus suitable for a broad range of applications in genetic and genomic research in Eucalyptus and possibly in related species of Myrtaceae, including genome sequencing, gene isolation, functional and comparative genomics. Because they have been constructed using the same tree (E. grandis BRASUZ1) whose full genome is being sequenced, they should prove instrumental for assembly and gap filling of the upcoming Eucalyptus reference genome sequence.

Combination of measures distinguishes pre-miRNAs from other stem-loops in the genome of the newly sequenced Anopheles darlingi.

BACKGROUND: Efforts using computational algorithms towards the enumeration of the full set of miRNAs of an organism have been limited by strong reliance on arguments of precursor conservation and feature similarity. However, miRNA precursors may arise anew or be lost across the evolutionary history of a species and a newly sequenced genome may be evolutionarily too distant from other genomes for an adequate comparative analysis. In addition, the learning of intricate classification rules based purely on features shared by miRNA precursors that are currently known may reflect a perpetuating identification bias rather than a sound means to tell true miRNAs from other genomic stem-loops. RESULTS: We show that there is a strong bias amongst annotated pre-miRNAs towards robust stem-loops in the genomes of Drosophila melanogaster and Anopheles gambiae and we propose a scoring scheme for precursor candidates which combines four robustness measures. Additionally, we identify several known pre-miRNA homologs in the newly sequenced Anopheles darlingi and show that most are found amongst the top-scoring precursor candidates. Furthermore, a comparison of the performance of our approach is made against two single-genome pre-miRNA classification methods. CONCLUSIONS: In this paper we present a strategy to sieve through the vast amount of stem-loops found in metazoan genomes in search of pre-miRNAs, significantly reducing the set of candidates while retaining most known miRNA precursors. This approach makes no use of conservation data and relies solely on properties derived from our knowledge of miRNA biogenesis.

CSA: an efficient algorithm to improve circular DNA multiple alignment.

BACKGROUND: The comparison of homologous sequences from different species is an essential approach to reconstruct the evolutionary history of species and of the genes they harbour in their genomes. Several complete mitochondrial and nuclear genomes are now available, increasing the importance of using multiple sequence alignment algorithms in comparative genomics. MtDNA has long been used in phylogenetic analysis and errors in the alignments can lead to errors in the interpretation of evolutionary information. Although a large number of multiple sequence alignment algorithms have been proposed to date, they all deal with linear DNA and cannot handle directly circular DNA. Researchers interested in aligning circular DNA sequences must first rotate them to the "right" place using an essentially manual process, before they can use multiple sequence alignment tools. RESULTS: In this paper we propose an efficient algorithm that identifies the most interesting region to cut circular genomes in order to improve phylogenetic analysis when using standard multiple sequence alignment algorithms. This algorithm identifies the largest chain of non-repeated longest subsequences common to a set of circular mitochondrial DNA sequences. All the sequences are then rotated and made linear for multiple alignment purposes.To evaluate the effectiveness of this new tool, three different sets of mitochondrial DNA sequences were considered. Other tests considering randomly rotated sequences were also performed. The software package Arlequin was used to evaluate the standard genetic measures of the alignments obtained with and without the use of the CSA algorithm with two well known multiple alignment algorithms, the CLUSTALW and the MAVID tools, and also the visualization tool SinicView. CONCLUSION: The results show that a circularization and rotation pre-processing step significantly improves the efficiency of public available multiple sequence alignment algorithms when used in the alignment of circular DNA sequences. The resulting alignments lead to more realistic phylogenetic comparisons between species.

Entropic Profiler - detection of conservation in genomes using information theory.

BACKGROUND: In the last decades, with the successive availability of whole genome sequences, many research efforts have been made to mathematically model DNA. Entropic Profiles (EP) were proposed recently as a new measure of continuous entropy of genome sequences. EP represent local information plots related to DNA randomness and are based on information theory and statistical concepts. They express the weighed relative abundance of motifs for each position in genomes. Their study is very relevant because under or over-representation segments are often associated with significant biological meaning. FINDINGS: The Entropic Profiler application here presented is a new tool designed to detect and extract under and over-represented DNA segments in genomes by using EP. It allows its computation in a very efficient way by recurring to improved algorithms and data structures, which include modified suffix trees. Available through a web interface http://kdbio.inesc-id.pt/software/ep/ and as downloadable source code, it allows to study positions and to search for motifs inside the whole sequence or within a specified range. DNA sequences can be entered from different sources, including FASTA files, pre-loaded examples or resuming a previously saved work. Besides the EP value plots, p-values and z-scores for each motif are also computed, along with the Chaos Game Representation of the sequence. CONCLUSION: EP are directly related with the statistical significance of motifs and can be considered as a new method to extract and classify significant regions in genomes and estimate local scales in DNA. The present implementation establishes an efficient and useful tool for whole genome analysis.

A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks.

BACKGROUND: The study of biological networks has led to the development of increasingly large and detailed models. Computer tools are essential for the simulation of the dynamical behavior of the networks from the model. However, as the size of the models grows, it becomes infeasible to manually verify the predictions against experimental data or identify interesting features in a large number of simulation traces. Formal verification based on temporal logic and model checking provides promising methods to automate and scale the analysis of the models. However, a framework that tightly integrates modeling and simulation tools with model checkers is currently missing, on both the conceptual and the implementational level. RESULTS: We have developed a generic and modular web service, based on a service-oriented architecture, for integrating the modeling and formal verification of genetic regulatory networks. The architecture has been implemented in the context of the qualitative modeling and simulation tool GNA and the model checkers NUSMV and CADP. GNA has been extended with a verification module for the specification and checking of biological properties. The verification module also allows the display and visual inspection of the verification results. CONCLUSIONS: The practical use of the proposed web service is illustrated by means of a scenario involving the analysis of a qualitative model of the carbon starvation response in E. coli. The service-oriented architecture allows modelers to define the model and proceed with the specification and formal verification of the biological properties by means of a unified graphical user interface. This guarantees a transparent access to formal verification technology for modelers of genetic regulatory networks.

Temporal logic patterns for querying dynamic models of cellular interaction networks.

MOTIVATION: Models of the dynamics of cellular interaction networks have become increasingly larger in recent years. Formal verification based on model checking provides a powerful technology to keep up with this increase in scale and complexity. The application of modelchecking approaches is hampered, however, by the difficulty for nonexpert users to formulate appropriate questions in temporal logic. RESULTS: In order to deal with this problem, we propose the use of patterns, that is, high-level query templates that capture recurring biological questions and can be automatically translated into temporal logic. The applicability of the developed set of patterns has been investigated by the analysis of an extended model of the network of global regulators controlling the carbon starvation response in Escherichia coli. AVAILABILITY: GNA and the model of the carbon starvation response network are available at http://www-helix.inrialpes.fr/gna.

An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance.

BACKGROUND: Motif finding algorithms have developed in their ability to use computationally efficient methods to detect patterns in biological sequences. However the posterior classification of the output still suffers from some limitations, which makes it difficult to assess the biological significance of the motifs found. Previous work has highlighted the existence of positional bias of motifs in the DNA sequences, which might indicate not only that the pattern is important, but also provide hints of the positions where these patterns occur preferentially. RESULTS: We propose to integrate position uniformity tests and over-representation tests to improve the accuracy of the classification of motifs. Using artificial data, we have compared three different statistical tests (Chi-Square, Kolmogorov-Smirnov and a Chi-Square bootstrap) to assess whether a given motif occurs uniformly in the promoter region of a gene. Using the test that performed better in this dataset, we proceeded to study the positional distribution of several well known cis-regulatory elements, in the promoter sequences of different organisms (S. cerevisiae, H. sapiens, D. melanogaster, E. coli and several Dicotyledons plants). The results show that position conservation is relevant for the transcriptional machinery. CONCLUSION: We conclude that many biologically relevant motifs appear heterogeneously distributed in the promoter region of genes, and therefore, that non-uniformity is a good indicator of biological relevance and can be used to complement over-representation tests commonly used. In this article we present the results obtained for the S. cerevisiae data sets.