PyCogent: a toolkit for making sense from sequence.
Ontology highlight
ABSTRACT:
SUBMITTER: Knight R
PROVIDER: S-EPMC2375001 | biostudies-literature | 2007
REPOSITORIES: biostudies-literature
Publications
PyCogent: a toolkit for making sense from sequence.
Knight Rob R Maxwell Peter P Birmingham Amanda A Carnes Jason J Caporaso J Gregory JG Easton Brett C BC Eaton Michael M Hamady Micah M Lindsay Helen H Liu Zongzhi Z Lozupone Catherine C McDonald Daniel D Robeson Michael M Sammut Raymond R Smit Sandra S Wakefield Matthew J MJ Widmann Jeremy J Wikman Shandy S Wilson Stephanie S Ying Hua H Huttley Gavin A GA
Genome biology 20070101 8
We have implemented in Python the COmparative GENomic Toolkit, a fully integrated and thoroughly tested framework for novel probabilistic analyses of biological sequences, devising workflows, and generating publication quality graphics. PyCogent includes connectors to remote databases, built-in generalized probabilistic techniques for working with biological sequences, and controllers for third-party applications. The toolkit takes advantage of parallel architectures and runs on a range of hardw ...[more]
Similar Datasets
Project description:A markedly reduced interest or pleasure in activities previously considered pleasurable is a main symptom in mood disorder and psychosis and is often present in other psychiatric disorders and neurodegenerative diseases. This condition can be labeled as "anhedonia," although in its most rigorous connotation the term refers to the lost capacity to feel pleasure that is one aspect of the complex phenomenon of processing and responding to reward. The responses to rewarding stimuli are relatively easy to study in rodents, and the experimental conditions that consistently and persistently impair these responses are used to model anhedonia. To this end, long-term exposure to environmental aversive conditions is primarily used, and the resulting deficits in reward responses are often accompanied by other deficits that are mainly reminiscent of clinical depressive symptoms. The different components of impaired reward responses induced by environmental aversive events can be assessed by different tests or protocols that require different degrees of time allocation, technical resources, and equipment. Rodent models of anhedonia are valuable tools in the study of the neurobiological mechanisms underpinning impaired behavioral responses and in the screening and characterization of drugs that may reverse these behavioral deficits. In particular, the antianhedonic or promotivational effects are relevant features in the spectrum of activities of drugs used in mood disorders or psychosis. Thus, more than the model, it is the choice of tests that is crucial since it influences which facets of anhedonia will be detected and should be tuned to the purpose of the study.
| S-EPMC6209858 | biostudies-other
Project description:Network analysis is a topic in secondary mathematics education of growing importance because it offers students an opportunity to understand how to model and solve many authentic technology and engineering problems. However, very little is known about how students make sense of the algorithms typically used in network analysis. In this study, I used the Hungarian algorithm to explore how students make sense of a network algorithm and how it can be used to solve assignment problems. I report the results of a design-based research project in which eight Year 12 students participated in a teaching experiment that spanned four 60-min lessons. A hypothetical learning trajectory was developed in which students were introduced to the steps of the Hungarian algorithm incrementally. The results suggest that students made sense of the intermediate steps of the algorithm, the results of those steps, and how the algorithm works to solve assignment problems. The difficulties that students encountered are also discussed.Supplementary informationThe online version contains supplementary material available at 10.1007/s10763-021-10180-3.
| S-EPMC8118110 | biostudies-literature
Project description:Fine scale genomic regulation is critical for maintaining genomic integrity and is often disrupted in neurodevelopmental disorders. An intriguing new study reveals the intricate biochemical complexity of de novo post-translational modifications of MeCP2, including activity-dependent protein-protein interactions that 'bridge' the nuclear receptor co-repressor (NCoR) complex to chromatin and lead to alterations in gene expression that characterize Rett syndrome.
| S-EPMC3817541 | biostudies-other
Project description:Systems biology approaches have been applied over the last two decades to study plant sulphur metabolism. These 'sulphur-omics' approaches have been developed in parallel with the advancing field of systems biology, which is characterized by permanent improvements of high-throughput methods to obtain system-wide data. The aim is to obtain a holistic view of sulphur metabolism and to generate models that allow predictions of metabolic and physiological responses. Besides known sulphur-responsive genes derived from previous studies, numerous genes have been identified in transcriptomics studies. This has not only increased our knowledge of sulphur metabolism but has also revealed links between metabolic processes, thus indicating a previously unexpected complex interconnectivity. The identification of response and control networks has been supported through metabolomics and proteomics studies. Due to the complex interlacing nature of biological processes, experimental validation using targeted or systems approaches is ongoing. There is still room for improvement in integrating the findings from studies of metabolomes, proteomes, and metabolic fluxes into a single unifying concept and to generate consistent models. We therefore suggest a joint effort of the sulphur research community to standardize data acquisition. Furthermore, focusing on a few different model plant systems would help overcome the problem of fragmented data, and would allow us to provide a standard data set against which future experiments can be designed and compared.
| S-EPMC6698701 | biostudies-literature
Project description:The meeting 'From sensory perception to motor output: genetic bases of behavior in the zebrafish embryo' was held at Minerve (South of France) on March 16-18, 2007. The meeting site was beautifully situated in the heart of the Minervois wine country, and its remoteness promoted conversations and interaction over the course of the program. The meeting covered neurogenesis and eye development on day 1, ear and lateral line development on day 2, and brain connectivity and behavior on day 3. Underlying all sessions, however, ran the growing importance of live imaging, an approach that takes full advantage of the transparency of fish embryos and early larvae, as illustrated by several movies and links in this report.
| S-EPMC1988804 | biostudies-other
Project description:Epigenetic research involves examining the mitotically heritable processes that regulate gene expression, independent of changes in the DNA sequence. Recent technical advances such as whole-genome bisulfite sequencing and affordable epigenomic array-based technologies, allow researchers to measure epigenetic profiles of large cohorts at a genome-wide level, generating comprehensive high-dimensional datasets that may contain important information for disease development and treatment opportunities. The epigenomic profile for a certain disease is often a result of the complex interplay between multiple genetic and environmental factors, which poses an enormous challenge to visualize and interpret these data. Furthermore, due to the dynamic nature of the epigenome, it is critical to determine causal relationships from the many correlated associations. In this review we provide an overview of recent data analysis approaches to integrate various omics layers to understand epigenetic mechanisms of complex diseases, such as obesity and cancer. We discuss the following topics: (i) advantages and limitations of major epigenetic profiling techniques, (ii) resources for standardization, annotation and harmonization of epigenetic data, and (iii) statistical methods and machine learning methods for establishing data-driven hypotheses of key regulatory mechanisms. Finally, we discuss the future directions for data integration that shall facilitate the discovery of epigenetic-based biomarkers and therapies.
| S-EPMC6390500 | biostudies-literature
Project description:OBJECTIVE: Cancer risk calculators on the internet have the potential to provide users with valuable information about their individual cancer risk. However, the lack of oversight of these sites raises concerns about low quality and inconsistent information. These concerns led us to evaluate internet cancer risk calculators. DESIGN: After a systematic search to find all cancer risk calculators on the internet, we reviewed the content of each site for information that users should seek to evaluate the quality of a website. We then examined the consistency of the breast cancer risk calculators by having 27 women complete 10 of the breast cancer risk calculators for themselves. We also completed the breast cancer risk calculators for a hypothetical high- and low-risk woman, and compared the output to Surveillance Epidemiology and End Results estimates for the average same-age and same-race woman. RESULTS: Nineteen sites were found, 13 of which calculate breast cancer risk. Most sites do not provide the information users need to evaluate the legitimacy of a website. The breast cancer calculator sites vary in the risk factors they assess to calculate breast cancer risk, how they operationalize each risk factor and in the risk estimate they provide for the same individual. CONCLUSIONS: Internet cancer risk calculators have the potential to provide a public health benefit by educating individuals about their risks and potentially encouraging preventive health behaviors. However, our evaluation of internet calculators revealed several problems that call into question the accuracy of the information that they provide. This may lead the users of these sites to make inappropriate medical decisions on the basis of misinformation.
| S-EPMC2359468 | biostudies-literature
Project description:Literature search is a routine practice for scientific studies as new discoveries build on knowledge from the past. Current tools (e.g. PubMed, PubMed Central), however, generally require significant effort in query formulation and optimization (especially in searching the full-length articles) and do not allow direct retrieval of specific statements, which is key for tasks such as comparing/validating new findings with previous knowledge and performing evidence attribution in biocuration. Thus, we introduce LitSense, which is the first web-based system that specializes in sentence retrieval for biomedical literature. LitSense provides unified access to PubMed and PMC content with over a half-billion sentences in total. Given a query, LitSense returns best-matching sentences using both a traditional term-weighting approach that up-weights sentences that contain more of the rare terms in the user query as well as a novel neural embedding approach that enables the retrieval of semantically relevant results without explicit keyword match. LitSense provides a user-friendly interface that assists its users to quickly browse the returned sentences in context and/or further filter search results by section or publication date. LitSense also employs PubTator to highlight biomedical entities (e.g. gene/proteins) in the sentences for better result visualization. LitSense is freely available at https://www.ncbi.nlm.nih.gov/research/litsense.
| S-EPMC6602490 | biostudies-literature
Project description:The B-cell lymphoma 2 (Bcl-2) family, comprised of pro- and anti-apoptotic proteins, regulates the delicate balance between programmed cell death and cell survival. The Bcl-2 family is essential in the maintenance of tissue homeostasis, but also a key culprit in tumorigenesis. Anti-apoptotic Bcl-2, the founding member of this family, was discovered due to its dysregulated expression in non-Hodgkin's lymphoma. Bcl-2 is a central protagonist in a wide range of human cancers, promoting cell survival, angiogenesis and chemotherapy resistance; this has prompted the development of Bcl-2-targeting drugs. Antisense oligonucleotides (ASO) are highly specific nucleic acid polymers used to modulate target gene expression. Over the past 25 years several Bcl-2 ASO have been developed in preclinical studies and explored in clinical trials. This review will describe the history and development of Bcl-2-targeted ASO; from initial attempts, optimizations, clinical trials undertaken and the promising candidates at hand.
| S-EPMC8778715 | biostudies-literature
Project description:Huntington disease (HD) is an autosomal dominant neurodegenerative disorder, characterized by motor, psychiatric and cognitive symptoms. HD is caused by a CAG repeat expansion in the first exon of the HTT gene, resulting in an expanded polyglutamine tract at the N-terminus of the huntingtin protein. Typical disease onset is around mid-life (adult-onset HD) whereas onset below 21 years is classified as juvenile HD. While much research has been done on the underlying HD disease mechanisms, little is known about regulation and expression levels of huntingtin RNA and protein.In this study we used 15 human post-mortem HD brain samples to investigate the expression of wild-type and mutant huntingtin mRNA and protein. In adult-onset HD brain samples, there was a small but significantly lower expression of mutant huntingtin mRNA compared to wild-type huntingtin mRNA, while wild-type and mutant huntingtin protein expression levels did not differ significantly. Juvenile HD subjects did show a lower expression of mutant huntingtin protein compared to wild-type huntingtin protein. Our results in HD brain and fibroblasts suggest that protein aggregation does not affect levels of huntingtin RNA and protein. Additionally, we did not find any evidence for a reduced expression of huntingtin antisense in fibroblasts derived from a homozygous HD patient.We found small differences in allelic huntingtin mRNA levels in adult-onset HD brain, with significantly lower mutant huntingtin mRNA levels. Wild-type and mutant huntingtin protein were not significantly different in adult-onset HD brain samples. Conversely, in juvenile HD brain samples mutant huntingtin protein levels were lower compared with wild-type huntingtin, showing subtle differences between juvenile HD and adult-onset HD. Since most HD model systems harbor juvenile repeat expansions, our results suggest caution with the interpretation of huntingtin mRNA and protein studies using HD cell and animal models with such long repeats. Furthermore, our huntingtin antisense results in homozygous HD cells do not support reduced huntingtin antisense expression due to an expanded CAG repeat.
| S-EPMC4411791 | biostudies-literature