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At least 1,063 records · Page 59Linked to original sources

PubMed2026

ViralQC: a tool for assessing completeness and contamination of predicted viral contigs.

MOTIVATION: Viruses represent the most abundant biological entities on Earth, playing vital roles in diverse ecosystems. Cataloging viruses across various environments is essential for understanding their properties and functions. Metagenomic sequencing has emerged as the most comprehensive method for virus discovery. However, distinguishing viral sequences from the vast background of microbial organisms in metagenomic data remains a significant challenge. Existing tools experience varying degrees of false positive rates due to noise in sequencing and assembly, and the integration of proviruses into microbial genomes. This highlights the urgent need for an accurate and efficient method to evaluate the quality of viral contigs. RESULTS: To address these challenges, we introduce ViralQC, a tool designed to assess the quality of viral contigs or bins. ViralQC identifies microbial contamination within putative viral sequences using an ensemble framework powered by DNA and protein foundation models and estimates completeness by analyzing protein organization. We evaluated ViralQC on multiple datasets and compared its performance against the state-of-the-art tool, CheckV. Leveraging both DNA and protein foundation models, ViralQC achieves higher sensitivity on contamination detection for contigs longer than 10 kbp while maintaining comparable accuracy. Additionally, ViralQC delivers more accurate estimation on contigs with completeness > 50%. AVAILABILITY: The source code of ViralQC is available via: https://github.com/ChengPENG-wolf/ViralQC.

Software↗

PubMed2026

pLAST-a tool for rapid comparison and classification of bacterial plasmid sequences.

MOTIVATION: The increasing number of fully sequenced bacterial plasmids being annotated and catalogued has prompted the development of computational tools for comparing and classifying them. Existing approaches typically compare full-length DNA sequences (e.g. Mash, BLASTn, and ANI-based methods) or translated open reading frames (ORFs) (e.g. DIAMOND), with plasmid-level scores obtained by aggregating ORF-to-ORF similarities; however, they are either restricted to closely related plasmids or become computationally demanding in large-scale analyses. RESULTS: We describe pLAST (plasmid Language Analysis and Search Tool), a plasmid-search tool built using word2vec representations of protein-family content informed by local genomic context. Benchmarks indicate that pLAST outperforms nucleotide-based methods and performs comparably to DIAMOND in identifying functionally similar plasmids and compared with the widely used Mash, it achieves 26% and 24% improvements in detecting shared mating-pair formation system type and relaxase type, respectively. This performance scales to database searches across hundreds of thousands of sequences, as demonstrated using the precomputed PlasmidScope collection of ∼750 000 plasmids. Beyond global similarity, pLAST also returns per-ORF plasmid-plasmid alignments, enabling detection of shared functional modules. AVAILABILITY AND IMPLEMENTATION: pLAST is freely accessible as a web server at https://plast.lbs.cent.uw.edu.pl/ or https://plast.lbs.biol.uw.edu.pl/ and available as a Python module along with a precomputed database at https://github.com/labstructbioinf/pLAST for customized analysis.

Plasmids↗

PubMed2003

Metabolomics spectral formatting, alignment and conversion tools (MSFACTs).

MOTIVATION: The amplified interest in metabolic profiling has generated the need for additional tools to assist in the rapid analysis of complex data sets. RESULTS: A new program; metabolomics spectral formatting, alignment and conversion tools, (MSFACTs) is described here for the automated import, reformatting, alignment, and export of large chromatographic data sets to allow more rapid visualization and interrogation of metabolomic data. MSFACTs incorporates two tools: one for the alignment of integrated chromatographic peak lists and another for extracting information from raw chromatographic ASCII formatted data files. MSFACTs is illustrated in the processing of GC/MS metabolomic data from different tissues of the model legume plant, Medicago truncatula. The results document that various tissues such as roots, stems, and leaves from the same plant can be easily differentiated based on metabolite profiles. Further, similar types of tissues within the same plant, such as the first to eleventh internodes of stems, could also be differentiated based on metabolite profiles. AVAILABILITY: Freely available upon request for academic and non-commercial use. Commercial use is available through licensing agreement http://www.noble.org/PlantBio/MS/MSFACTs/MSFACTs.html.

Cluster Analysis↗

PubMed2004

Taverna: a tool for the composition and enactment of bioinformatics workflows.

MOTIVATION: In silico experiments in bioinformatics involve the co-ordinated use of computational tools and information repositories. A growing number of these resources are being made available with programmatic access in the form of Web services. Bioinformatics scientists will need to orchestrate these Web services in workflows as part of their analyses. RESULTS: The Taverna project has developed a tool for the composition and enactment of bioinformatics workflows for the life sciences community. The tool includes a workbench application which provides a graphical user interface for the composition of workflows. These workflows are written in a new language called the simple conceptual unified flow language (Scufl), where by each step within a workflow represents one atomic task. Two examples are used to illustrate the ease by which in silico experiments can be represented as Scufl workflows using the workbench application.

Computational Biology↗

PubMed2004

DNAfan: a software tool for automated extraction and analysis of user-defined sequence regions.

SUMMARY: DNAfan (DNA Feature ANalyzer) is a tool combining sequence-filtering and pattern searching. DNAfan automatically extracts user-defined sets of sequence fragments from large sequence sets. Fragments are defined by annotated gene feature keys and co- or non-occurring patterns within the feature or close to it. A gene feature parser and a pattern-based filter tool localizes and extracts the specific subset of sequences. The selected sequence data can subsequently be retrieved for analyses or further processed with DNAfan to find the occurrence of specific patterns or structural motifs. DNAfan is a powerful tool for pattern analysis. Its filter features restricts the pattern search to a well-defined set of sequences, allowing drastic reduction in false positive hits. AVAILABILITY: http://bighost.ba.itb.cnr.it:8080/Framework.

Algorithms↗

PubMed2005

MAGIC Tool: integrated microarray data analysis.

SUMMARY: Several programs are now available for analyzing the large datasets arising from cDNA microarray experiments. Most programs are expensive commercial packages or require expensive third party software. Some are freely available to academic researchers, but are limited to one operating system. MicroArray Genome Imaging and Clustering Tool (MAGIC Tool) is an open source program that works on all major platforms, and takes users 'from tiff to gif'. Several unique features of MAGIC Tool are particularly useful for research and teaching. AVAILABILITY: http://www.bio.davidson.edu/MAGIC

Algorithms↗

PubMed2006

Tools for the SBML Community.

MOTIVATION: SBML is quickly becoming the standard format to exchange biochemical models. The tools presented in this paper are loosely-coupled, and are intended to be incorporated into SBML aware applications. The rationale for this is to reduce the amount of repeated work carried out within the community and to create tools that offer a greater number of features to the end-user. AVAILABILITY: All tools described are available from http://www.basis.ncl.ac.uk/software and are licensed under GNU General Public License.

Biochemistry↗

PubMed2006

An interactive power analysis tool for microarray hypothesis testing and generation.

MOTIVATION: Human clinical projects typically require a priori statistical power analyses. Towards this end, we sought to build a flexible and interactive power analysis tool for microarray studies integrated into our public domain HCE 3.5 software package. We then sought to determine if probe set algorithms or organism type strongly influenced power analysis results. RESULTS: The HCE 3.5 power analysis tool was designed to import any pre-existing Affymetrix microarray project, and interactively test the effects of user-defined definitions of alpha (significance), beta (1-power), sample size and effect size. The tool generates a filter for all probe sets or more focused ontology-based subsets, with or without noise filters that can be used to limit analyses of a future project to appropriately powered probe sets. We studied projects from three organisms (Arabidopsis, rat, human), and three probe set algorithms (MAS5.0, RMA, dChip PM/MM). We found large differences in power results based on probe set algorithm selection and noise filters. RMA provided high sensitivity for low numbers of arrays, but this came at a cost of high false positive results (24% false positive in the human project studied). Our data suggest that a priori power calculations are important for both experimental design in hypothesis testing and hypothesis generation, as well as for the selection of optimized data analysis parameters. AVAILABILITY: The Hierarchical Clustering Explorer 3.5 with the interactive power analysis functions is available at www.cs.umd.edu/hcil/hce or www.cnmcresearch.org/bioinformatics. CONTACT: jseo@cnmcresearch.org

Algorithms↗

PubMed2006

K-Fold: a tool for the prediction of the protein folding kinetic order and rate.

UNLABELLED: K-Fold is a tool for the automatic prediction of the protein folding kinetic order and rate. The tool is based on a support vector machine (SVM) that was trained on a data set of 63 proteins, whose 3D structure and folding mechanism are known from experiments already described in the literature. The method predicts whether a protein of known atomic structure folds according to a two-state or a multi-state kinetics and correctly classifies 81% of the folding mechanisms when tested over the training set of the 63 proteins. It also predicts as a further option the logarithm of the folding rate. To the best of our knowledge, the tool discriminates for the first time whether a protein is characterized by a two state or a multiple state kinetics, during the folding process, and concomitantly estimates also the value of the constant rate of the process. When used to predict the logarithm of the folding rate, K-Fold scores with a correlation value to the experimental data of 0.74 (with a SE of 1.2). AVAILABILITY: http://gpcr.biocomp.unibo.it/cgi/predictors/K-Fold/K-Fold.cgi. SUPPLEMENTARY INFORMATION: http://gpcr.biocomp.unibo.it/~emidio/K-Fold/K-Fold_help.html.

Algorithms↗

PubMed2002

The final version of the Patient Perspective Survey (PPS): a new tool to improve consultation outcome and patient participation in general practice patients with complex health problems. Doctors' and patients' evaluation and guidelines for clinical use.

BACKGROUND: The Patient Perspective Survey (PPS) is a new clinical communication tool designed to stimulate patient involvement in the management of complex health problems in general practice and to improve patient and doctor satisfaction with the consultation. The development of this final 38-item version of the PPS has been described elsewhere. OBJECTIVE: The aims of this article are to present recommendations for clinical use and how GPs and patients have evaluated this new tool. METHODS: The study material included 159 patients (78% females) with a mean age of 45 years, mainly presenting with longstanding musculoskeletal and psychosocial disorders, selected by 32 GPs. After the PPS-based consultation, both doctor and patient were asked to fill in evaluation forms. RESULTS: In as many as 55-85% of the consultations' various aspects, it was perceived by the GPs that the use of the survey helped (to some extent, much or very much) in achieving improved clinical communication and a constructive consultation. The most important elements appeared to be stimulation of positive interaction/processes and obtaining new and relevant information. Similar results were found regarding patient evaluation. There was significantly more positive doctor evaluation if the doctor-patient relationship had lasted less than 1 year, and if the patient agreed to prepare a 'plan of action' for a follow-up consultation. Guidelines for clinical use are presented. CONCLUSION: We now regard the PPS to be completed for daily clinical use and believe that it has been shown to be a potent tool to improve consultation outcome in the large and challenging group of patients with complex health problems in general practice.

Adult↗

PubMed2004

Emerging technologies: trendy RNA tools for aging research.

Aging is an inevitable biological phenomenon. Attempts to understand its mechanisms and, consequently, to therapeutically decelerate or even reverse the process are limited by its daunting complexity. Rapid and robust functional genomic tools suited to a wide array of experimental model systems are needed to dissect the interplay of individual genes during aging. In this article, we review principles that transcend the view of RNA, from a molecule merely mediating the flow of genetic information, into a unique molecular tool. In the form of catalytic molecular scissors (ribozymes), antibody-like antagonists (aptamers) and gene silencers (interfering RNAs, RNAi) can be effectively used to dissect biofunctions conserved throughout the evolution. In this review, application of recent RNA tools in aging research is discussed.

Aging↗

PubMed2001

Tools for monitoring the effectiveness of district maternity referral systems.

It is widely accepted that substantial reductions in maternal mortality and severe morbidity are impossible to achieve without an effective referral system for complicated cases. Early detection and referral to higher levels of care might also substantially reduce neonatal deaths due to the complications of childbirth. The general goal of such a referral system is that patients are dealt with in the right place with effective treatment provided at the minimum of cost. There are real challenges, however, in monitoring the effectiveness of such referral systems once put in place. This paper describes some of the tools used to review pregnancy-related referrals in Lusaka, Zambia. The tool-mix used provided information for monitoring five different aspects of the referral system: the distribution of births across levels of facility and population coverage; the use of essential obstetric care (EOC) level facilities by women with complications; the progress towards a reduction of maternal mortality at referral facility level; inappropriate use of EOC level facility; and perinatal outcomes at peripheral facility level. Apart from the information on coverage, the data came from routinely collected facility statistics, registers and medical notes. Findings for Lusaka are reported. Consideration is given to issues of interpretation of specific indicators, and to how such tools might be used in conjunction with others, in order to help district managers to monitor the effectiveness of district maternity referral systems.

Female↗

PubMed2004

Evaluating community coalition characteristics and functioning: a summary of measurement tools.

Community coalitions and partnerships are frequently used to promote community health; however, little research to evaluate measurement tools for assessing their effectiveness has been reported. This summary identified measurement tools for coalition or partnership characteristics and functioning. The largest numbers of measures were identified for assessing individual and group characteristics, with impact and outcome measures being the least numerous. Published measures often lacked information regarding validity and reliability, with internal consistency reliability being the most commonly reported statistic. Some measures were well defined, but others lacked conceptual clarity. Valid and reliable tools that can be applied across multiple coalitions are necessary in order to achieve a better understanding of the associations among factors influencing optimal coalition functioning and community health impacts and outcomes.

Community Health Planning↗

PubMed1998

Landscape ecology and epidemiology of vector-borne diseases: tools for spatial analysis.

Geographic information systems (GIS), global positioning systems (GPS), remote sensing, and spatial statistics are tools to analyze and integrate the spatial component in epidemiology of vector-borne disease into research, surveillance, and control programs based on a landscape ecology approach. Landscape ecology, which deals with the mosaic structure of landscapes and ecosystems, considers the spatial heterogeneity of biotic and abiotic components as the underlying mechanism which determines the structure of ecosystems. The methodologies of GIS, GPS, satellite imagery, and spatial statistics, and the landscape ecology--epidemiology approach are described, and applications of these methodologies to vector-borne diseases are reviewed. Collaborative studies by the author and colleagues on malaria in Israel and tsetse flies in Kenya, and Lyme disease, LaCrosse encephalitis, and eastern equine encephalitis in the north-central United States are presented as examples for application of these tools to research and disease surveillance. Relevance of spatial tools and landscape ecology to emerging infectious diseases and to studies of global change effects on vector-borne diseases are discussed.

Animals↗

PubMed2003

The Diet Quality Index-International (DQI-I) provides an effective tool for cross-national comparison of diet quality as illustrated by China and the United States.

A composite measure of diet has been preferred to an index of a single nutrient or food in the area of dietary assessment. However, the lack of such a tool for cross-national comparisons has restricted the ability to compare diet quality between countries using an overall measure of diet. In this study, we created a tool called the Diet Quality Index-International (DQI-I) for global monitoring and exploration of diet quality across countries. The major categories of the index components are variety, adequacy, moderation and overall balance. Using the tool, this research presents a cross-national comparison of diet quality between China and the United States, incorporating comparable national in-depth diet data. The mean of the DQI-I score was slightly higher in China than in the United States. By major categories of the DQI-I, dietary variety was better achieved in the U.S. diet; moderation and overall balance of intakes were better accomplished in China. The DQI-I was successful in capturing variability in intakes of food and nutrients in both countries. Some distinct patterns of poor quality diet in each country were also identified. As demonstrated in this study, the DQI-I provides an effective means of cross-national comparative work for global understanding of diet quality. Furthermore, the dietary problem areas identified by the DQI-I may be useful in guiding the development of programs to improve public health.

China↗

PubMed1991

Software tools for analyzing pairwise alignments of long sequences.

Pairwise comparison of long stretches of genomic DNA sequence can identify regions conserved across species, which often indicate functional significance. However, the novel insights frequently must be windowed from a flood of information; for instance, running an alignment program on two 50-kilobase sequences might yield over a hundred pages of alignments. Direct inspection of such a volume of printed output is infeasible, or at best highly undesirable, and computer tools are needed to summarize the information, to assist in its analysis, and to report the findings. This paper describes two such software tools. One tool prepares publication-quality pictorial representations of alignments, while another facilitates interactive browsing of pairwise alignment data. Their effectiveness is illustrated by comparing the beta-like globin gene clusters between humans and rabbits. A second example compares the chloroplast genomes of tobacco and liverwort.

Animals↗

PubMed2000

Web-based visualization tools for bacterial genome alignments.

With the increase in the flow of sequence data, both in contigs and whole genomes, visual aids for comparison and analysis studies are becoming imperative. We describe three web-based tools for visualizing alignments of bacterial genomes. The first, called Enteric, produces a graphical, hypertext view of pairwise alignments between a reference genome and sequences from each of several related organisms, covering 20 kb around a user-specified position. Insertions, deletions and rearrangements relative to the reference genome are color-coded, which reveals many intriguing differences among genomes. The second, Menteric, computes and displays nucleotide-level multiple alignments of the same sequences, together with annotations of ORFs and regulatory sites, in a 1 kb region surrounding a given address. The third, a Java-based viewer called Maj, combines some features of the previous tools, and adds a zoom-in mechanism. We compare the Escherichia coli K-12 genome with the partially sequenced genomes of Klebsiella pneumoniae, Yersinia pestis, Vibrio cholerae, and the Salmonella enterica serovars Typhimurium, Typhi and Paratyphi A. Examination of the pairwise and multiple alignments in a region allows one to draw inferences about regulatory patterns and functional assignments. For example, these tools revealed that rffH, a gene involved in enterobacterial common antigen (ECA) biosynthesis, is partly deleted in one of the genomes. We used PCR to show that this deletion occurs sporadically in some strains of some serovars of S.enterica subspecies I but not in any strains tested from six other subspecies. The resulting cell surface diversity may be associated with selection by the host immune response.

DNA, Bacterial↗

PubMed2003

TRANSPATH: an integrated database on signal transduction and a tool for array analysis.

TRANSPATH is a database system about gene regulatory networks that combines encyclopedic information on signal transduction with tools for visualization and analysis. The integration with TRANSFAC, a database about transcription factors and their DNA binding sites, provides the possibility to obtain complete signaling pathways from ligand to target genes and their products, which may themselves be involved in regulatory action. As of July 2002, the TRANSPATH Professional release 3.2 contains about 9800 molecules, >1800 genes and >11 400 reactions collected from approximately 5000 references. With the ArrayAnalyzer, an integrated tool has been developed for evaluation of microarray data. It uses the TRANSPATH data set to identify key regulators in pathways connected with up- or down-regulated genes of the respective array. The key molecules and their surrounding networks can be viewed with the PathwayBuilder, a tool that offers four different modes of visualization. More information on TRANSPATH is available at http://www.biobase.de/pages/products/databases.html.

Animals↗