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  • 1
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    Breaking-Cas--interactive design of guide RNAs for CRISPR-Cas experiments for ENSEMBL genomes (2016)
    Oxford University Press
    Details
    Publication Date: 2016-07-06
    Description: The CRISPR/Cas technology is enabling targeted genome editing in multiple organisms with unprecedented accuracy and specificity by using RNA-guided nucleases. A critical point when planning a CRISPR/Cas experiment is the design of the guide RNA (gRNA), which directs the nuclease and associated machinery to the desired genomic location. This gRNA has to fulfil the requirements of the nuclease and lack homology with other genome sites that could lead to off-target effects. Here we introduce the Breaking-Cas system for the design of gRNAs for CRISPR/Cas experiments, including those based in the Cas9 nuclease as well as others recently introduced. The server has unique features not available in other tools, including the possibility of using all eukaryotic genomes available in ENSEMBL (currently around 700), placing variable PAM sequences at 5' or 3' and setting the guide RNA length and the scores per nucleotides. It can be freely accessed at: http://bioinfogp.cnb.csic.es/tools/breakingcas , and the code is available upon request.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    MBROLE 2.0--functional enrichment of chemical compounds (2016)
    Oxford University Press
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    Publication Date: 2016-07-06
    Description: Metabolites Biological Role (MBROLE) is a server that performs functional enrichment analysis of a list of chemical compounds derived from a metabolomics experiment, which allows this list to be interpreted in biological terms. Since its release in 2011, MBROLE has been used by different groups worldwide to analyse metabolomics experiments from a variety of organisms. Here we present the latest version of the system, MBROLE2, accessible at http://csbg.cnb.csic.es/mbrole2 . MBROLE2 has been supplemented with 10 databases not available in the previous version, which allow analysis over a larger, richer set of vocabularies including metabolite–protein and drug–protein interactions. This new version performs automatic conversion of compound identifiers from different databases, thus simplifying usage. In addition, the user interface has been redesigned to generate an interactive, more intuitive representation of the results.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Characterization of clinical signs in the human interactome (2016)
    Oxford University Press
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    Publication Date: 2016-06-16
    Description: Motivation : Many diseases are related by shared associated molecules and pathways, exhibiting comorbidities and common phenotypes, an indication of the continuous nature of the human pathological landscape. Although it is continuous, this landscape is always partitioned into discrete diseases when studied at the molecular level. Clinical signs are also important phenotypic descriptors that can reveal the molecular mechanisms that underlie pathological states, but have seldom been the subject of systemic research. Here, we quantify the modular nature of the clinical signs associated with genetic diseases in the human interactome. Results : We found that clinical signs are reflected as modules at the molecular network level, to at least to the same extent as diseases. They can thus serve as a valid complementary partition of the human pathological landscape, with implications for etiology research, diagnosis and treatment. Contact: monica.chagoyen@cnb.csic.es Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 4
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    Detection of significant protein coevolution (2015)
    Oxford University Press
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    Publication Date: 2015-06-27
    Description: Motivation: The evolution of proteins cannot be fully understood without taking into account the coevolutionary linkages entangling them. From a practical point of view, coevolution between protein families has been used as a way of detecting protein interactions and functional relationships from genomic information. The most common approach to inferring protein coevolution involves the quantification of phylogenetic tree similarity using a family of methodologies termed mirrortree. In spite of their success, a fundamental problem of these approaches is the lack of an adequate statistical framework to assess the significance of a given coevolutionary score (tree similarity). As a consequence, a number of ad hoc filters and arbitrary thresholds are required in an attempt to obtain a final set of confident coevolutionary signals. Results: In this work, we developed a method for associating confidence estimators ( P values) to the tree-similarity scores, using a null model specifically designed for the tree comparison problem. We show how this approach largely improves the quality and coverage (number of pairs that can be evaluated) of the detected coevolution in all the stages of the mirrortree workflow, independently of the starting genomic information. This not only leads to a better understanding of protein coevolution and its biological implications, but also to obtain a highly reliable and comprehensive network of predicted interactions, as well as information on the substructure of macromolecular complexes using only genomic information. Availability and implementation: The software and datasets used in this work are freely available at: http://csbg.cnb.csic.es/pMT/ . Contact: pazos@cnb.csic.es Supplementary Information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 5
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    JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures (2012)
    Oxford University Press
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    Publication Date: 2012-02-17
    Description: : We have implemented in a single package all the features required for extracting, visualizing and manipulating fully conserved positions as well as those with a family-dependent conservation pattern in multiple sequence alignments. The program allows, among other things, to run different methods for extracting these positions, combine the results and visualize them in protein 3D structures and sequence spaces. Availability and implementation: JDet is a multiplatform application written in Java. It is freely available, including the source code, at http://csbg.cnb.csic.es/JDet . The package includes two of our recently developed programs for detecting functional positions in protein alignments ( Xdet and S3Det ), and support for other methods can be added as plug-ins. A help file and a guided tutorial for JDet are also available. Contact: pazos@cnb.csic.es
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 6
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    Practical analysis of specificity-determining residues in protein families (2016)
    Oxford University Press
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    Publication Date: 2016-03-17
    Description: Determining the residues that are important for the molecular activity of a protein is a topic of broad interest in biomedicine and biotechnology. This knowledge can help understanding the protein’s molecular mechanism as well as to fine-tune its natural function eventually with biotechnological or therapeutic implications. Some of the protein residues are essential for the function common to all members of a family of proteins, while others explain the particular specificities of certain subfamilies (like binding on different substrates or cofactors and distinct binding affinities). Owing to the difficulty in experimentally determining them, a number of computational methods were developed to detect these functional residues, generally known as ‘specificity-determining positions’ (or SDPs), from a collection of homologous protein sequences. These methods are mature enough for being routinely used by molecular biologists in directing experiments aimed at getting insight into the functional specificity of a family of proteins and eventually modifying it. In this review, we summarize some of the recent discoveries achieved through SDP computational identification in a number of relevant protein families, as well as the main approaches and software tools available to perform this type of analysis.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
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  • 7
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    Resource-defense polygyny and self-limitation of population density in free-ranging guanacos (2016)
    Oxford University Press
    Details
    Publication Date: 2016-05-12
    Description: Although ecologists and managers have been increasingly preoccupied with the crowding consequences of overabundant herbivores, the potential role of territorial behavior as a self-regulatory agent has seldom been considered. The crowding mechanism underlies most regulation models in ungulate demography and relies on the assumption of an equal share of available supplies among individuals. In contrast, in territorial systems dominant individuals monopolize resources, predicting deviations from the expected demographic outcomes under the crowding approach. We used empirical data on a protected guanaco ( Lama guanicoe ) population to test competing hypotheses about crowding and territorial defense as the mechanism driving density regulation in a resource-defense polygyny ungulate. We assessed density dependence on recruitment at different spatial scales and density effects on preferred forage availability. The guanaco density inside the reserve increased rapidly and then stabilized during the last third of the study period. The absence of density effects on recruitment questions the existence of crowding mechanisms. Guanaco numbers stabilized below the environmental carrying capacity predicted by an equal share of available forage, supporting territorial defense as the mechanism shaping population density in the area. Variability in forage cover was independent from changes in population density, rejecting crowding effects on food supplies. These results are consistent with the hypothesis of a self-regulatory mechanism derived from resource defense that may prevent overgrazing. Our findings suggest that other factors in addition to food availability may determine the demographic carrying capacity under resource defense systems, stressing the importance of accounting for behavioral traits when addressing management issues.
    Print ISSN: 1045-2249
    Electronic ISSN: 1465-7279
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    COPRED: prediction of fold, GO molecular function and functional residues at the domain level (2013)
    Oxford University Press
    Details
    Publication Date: 2013-07-06
    Description: : Only recently the first resources devoted to the functional annotation of proteins at the domain level started to appear. The next step is to develop specific methodologies for predicting function at the domain level based on these resources, and to implement them in web servers to be used by the community. In this work, we present COPRED, a web server for the concomitant prediction of fold, molecular function and functional sites at the domain level, based on a methodology for domain molecular function prediction and a resource of domain functional annotations previously developed and benchmarked. Availability and implementation: COPRED can be freely accessed at http://csbg.cnb.csic.es/copred . The interface works in all standard web browsers. WebGL (natively supported by most browsers) is required for the in-line preview and manipulation of protein 3D structures. The website includes a detailed help section and usage examples. Contact: pazos@cnb.csic.es
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 9
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    Cloud-Based Personalization of New Advertising and e-Commerce Models for Video Consumption (2013)
    Oxford University Press
    Details
    Publication Date: 2013-04-27
    Description: Over the last few years, we have witnessed a generalization of the consumption of video contents through different media (computers, television, mobile phones, tablets,...) that converge into a unified user experience in an (almost) all-IP technological environment. At the same time, there have been significant advances in the generation and characterization of multimedia contents, due to the advent of social networking and the consolidation of standards like moving picture experts group (MPEG)-4 and MPEG-7. Finally, it is becoming easier and more natural to interact with multimedia contents, thanks to devices like tactile screens and touchpads. Overall, this landscape enables great possibilities for advertising and e-commerce, far beyond the traditional business models of broadcast TV. In this paper, we present a novel realization of two non-invasive advertising and e-commerce models to exploit those possibilities, grounded on a cloud-based personalization engine. This system cannot only identify the most interesting products to advertise to each user at any time, but also compose personalized applications on the fly, ready to run on different consumer device platforms. Our experiments show that this proposal can be very positively perceived by the end users.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Published by Oxford University Press
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  • 10
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    Tools for the functional interpretation of metabolomic experiments (2013)
    Oxford University Press
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    Publication Date: 2013-11-10
    Description: The so-called ‘omics’ approaches used in modern biology aim at massively characterizing the molecular repertories of living systems at different levels. Metabolomics is one of the last additions to the ‘omics’ family and it deals with the characterization of the set of metabolites in a given biological system. As metabolomic techniques become more massive and allow characterizing larger sets of metabolites, automatic methods for analyzing these sets in order to obtain meaningful biological information are required. Only recently the first tools specifically designed for this task in metabolomics appeared. They are based on approaches previously used in transcriptomics and other ‘omics’, such as annotation enrichment analysis. These, together with generic tools for metabolic analysis and visualization not specifically designed for metabolomics will for sure be in the toolbox of the researches doing metabolomic experiments in the near future.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
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