PASTA: splice junction identification from RNA-Sequencing data

Background: Next generation transcriptome sequencing (RNA-Seq) is emerging as a powerful experimental tool for the study of alternative splicing and its regulation, but requires ad-hoc analysis methods and tools. PASTA (Patterned Alignments for Splicing and Transcriptome Analysis) is a splice junction detection algorithm specifically designed for RNA-Seq data, relying on a highly accurate alignment strategy and on a combination of heuristic and statistical methods to identify exon-intron junctions with high accuracy. Results: Comparisons against TopHat and other splice junction prediction software on real and simulated datasets show that PASTA exhibits high specificity and sensitivity, especially at lower coverage levels. Moreover, PASTA is highly configurable and flexible, and can therefore be applied in a wide range of analysis scenarios: it is able to handle both single-end and paired-end reads, it does not rely on the presence of canonical splicing signals, and it uses organism-specific regression models to accurately identify junctions. Conclusions: PASTA is a highly efficient and sensitive tool to identify splicing junctions from RNA-Seq data. Compared to similar programs, it has the ability to identify a higher number of real splicing junctions, and provides highly annotated output files containing detailed information about their location and characteristics. Accurate junction data in turn facilitates the reconstruction of the splicing isoforms and the analysis of their expression levels, which will be performed by the remaining modules of the PASTA pipeline, still under development. Use of PASTA can therefore enable the large-scale investigation of transcription and alternative splicing

A SNP-centric database for the investigation of the human genome

BACKGROUND: Single Nucleotide Polymorphisms (SNPs) are an increasingly important tool for genetic and biomedical research. Although current genomic databases contain information on several million SNPs and are growing at a very fast rate, the true value of a SNP in this context is a function of the quality of the annotations that characterize it. Retrieving and analyzing such data for a large number of SNPs often represents a major bottleneck in the design of large-scale association studies. DESCRIPTION: SNPper is a web-based application designed to facilitate the retrieval and use of human SNPs for high-throughput research purposes. It provides a rich local database generated by combining SNP data with the Human Genome sequence and with several other data sources, and offers the user a variety of querying, visualization and data export tools. In this paper we describe the structure and organization of the SNPper database, we review the available data export and visualization options, and we describe how the architecture of SNPper and its specialized data structures support high-volume SNP analysis. CONCLUSIONS: The rich annotation database and the powerful data manipulation and presentation facilities it offers make SNPper a very useful online resource for SNP research. Its success proves the great need for integrated and interoperable resources in the field of computational biology, and shows how such systems may play a critical role in supporting the large-scale computational analysis of our genome

Moment-based metrics for global sensitivity analysis of hydrological systems

We propose new metrics to assist global sensitivity analysis, GSA, of hydrological and Earth systems. Our approach allows assessing the impact of uncertain parameters on main features of the probability density function, pdf, of a target model output, y. These include the expected value of y, the spread around the mean and the degree of symmetry and tailedness of the pdf of y. Since reliable assessment of higher order statistical moments can be computationally demanding, we couple our GSA approach with a surrogate model, approximating the full model response at a reduced computational cost. Here, we consider the generalized Polynomial Chaos Expansion (gPCE), other model reduction techniques being fully compatible with our theoretical framework. We demonstrate our approach through three test cases, including an analytical benchmark, a simplified scenario mimicking pumping in a coastal aquifer, and a laboratory-scale conservative transport experiment. Our results allow ascertaining which parameters can impact some moments of the model output pdf while being uninfluential to others. We also investigate the error associated with the evaluation of our sensitivity metrics by replacing the original system model through a gPCE. Our results indicate that the construction of a surrogate model with increasing level of accuracy might be required depending on the statistical moment considered in the GSA. Our approach is fully compatible with (and can assist the development of) analysis techniques employed in the context of reduction of model complexity, model calibration, design of experiment, uncertainty quantification and risk assessment

Le acque sotterranee del Cansiglio

Il Cansiglio è un altipiano carsico, con un’estensione di circa 100 km2 e un’altitudine media di circa 1000 m; esso è situato al confine tra due regioni (Veneto e Friuli Venezia Giulia) e tre provincie (Treviso, Belluno e Pordenone). Questo importante sistema carsico non è mai stato oggetto di approfonditi studi idrogeologici, nonostante la presenza di rilevanti sorgenti alla sua base (Meschio, Molinetto, Santissima e Gorgazzo). L’occasione si è presentata con l’esplorazione, da parte del Gruppo Speleologico Ferrarese in collaborazione con altri gruppi speleologici, di quella che è tuttora la grotta più profonda della zona: l’Abisso Col de la Rizza (904/FR410) (circa 800 m di profondità per 4 km di sviluppo). Con la collaborazione del Dipartimento di Scienze della Terra dell’Università di Ferrara, è stato, quindi, progettato e realizzato un multi- tracciamento delle acque sotterranee, con due iniezioni in parallelo: fluoresceina sodica all’Abisso Col de la Rizza e tinopal CBS-X al Bus de la Genziana (V-TV1000) (la cavità più sviluppata della zona, con circa 5 km di sviluppo per 600 m di profondità). Il monitoraggio è stato eseguito alle sorgenti del Molinetto, Santissima e Gorgazzo, mediante campionatori di acqua automatici (alle sorgenti Molinetto e Gorgazzo) e con un impegnativo programma di prelievi manuali di campioni d’acqua e di fluocaptori (carboni attivi e garze di cotone) in 3-4 punti di ogni sorgente monitorata. Al termine del tracciamento risultavano positive alla fluoresceina sodica le sorgenti Molinetto e Santissima, mentre nessuna delle sorgenti monitorate era positiva al tinopal CBS-X. Le curve di arrivo del tracciante, permettevano il calcolo delle velocità medie di transito in entrambe le sorgenti positive alla fluoresceina sodica, pari a circa: 250 m giorno-1, in fase di magra, e 1100 m giorno-1, in fase di piena.Cansiglio is a limestone plateau with an extent of about 100 km2 and a mean altitude of 1000 m; it is located on the border between two regions (Veneto and Friuli Venezia Giulia) and three provinces (Treviso, Belluno and Pordenone). The hydrogeology of this important karst system is poorly known, despite it probably feeds three important springs located at its south-eastern border (Molinetto, Santissima and Gorgazzo) that form Livenza River. Gruppo Speleologico Ferrarese, in collaboration with other speleological team, explored the deepest cave of Cansiglio: Abisso Col de la Rizza (904/FR410) (about 800 m deep and with 4 km of extent), which provided the opportunity to perform a tracer test. In collaboration with the Earth Sciences Department of Ferrara University, a multi-tracer test was made with two contemporary injections of fluorescent dyes in groundwaters: uranine in Abisso Col de la Rizza and tinopal CBS-X in Bus de la Genziana (V-TV1000) (600 m deep and 5 km of extent). The monitoring at Molinetto, Santissima and Gorgazzo springs was performed by means of automated samplers (at Gorgazzo and Molinetto springs) and an intense discrete sampling survey, which included water samples, charcoal bags and cotton lints collection. Molinetto and Santissima springs resulted positive to uranine, while any springs was positive to tinopal CBS-X. The breakthrough curves make possible the determination of the mean velocity of uranine: about 250 m day-1, during low flow conditions, and 1100 m day-1, after an intense rainfall event

Phenotypic and genotypic data integration and exploration through a web-service architecture

<p>Abstract</p> <p>Background</p> <p>Linking genotypic and phenotypic information is one of the greatest challenges of current genetics research. The definition of an Information Technology infrastructure to support this kind of studies, and in particular studies aimed at the analysis of complex traits, which require the definition of multifaceted phenotypes and the integration genotypic information to discover the most prevalent diseases, is a paradigmatic goal of Biomedical Informatics. This paper describes the use of Information Technology methods and tools to develop a system for the management, inspection and integration of phenotypic and genotypic data.</p> <p>Results</p> <p>We present the design and architecture of the Phenotype Miner, a software system able to flexibly manage phenotypic information, and its extended functionalities to retrieve genotype information from external repositories and to relate it to phenotypic data. For this purpose we developed a module to allow customized data upload by the user and a SOAP-based communications layer to retrieve data from existing biomedical knowledge management tools. In this paper we also demonstrate the system functionality by an example application of the system in which we analyze two related genomic datasets.</p> <p>Conclusion</p> <p>In this paper we show how a comprehensive, integrated and automated workbench for genotype and phenotype integration can facilitate and improve the hypothesis generation process underlying modern genetic studies.</p

Towards a better knowledge of Cansiglio karst system (Italy): results of the first successful groundwater tracer test

Cansiglio is a limestone plateau located on the border between the regions of Veneto and Friuli-Venezia Giulia, northeastern Italy. The eastern area is characterized by a thick succession of Cretaceous peritidal carbonates, while the central western part is characterized by slope breccia deposits. Even thoughPian Cansiglio is an important karst system, its hydrogeology is poorly known. Three important springs that form the Livenza River are located at its southeastern border and are thought to represent the majority of karst aquifer discharge, but no experimental data are available in the literature. Gruppo Speleologico Ferrarese explored an 800 m deep cave (Abisso Col de la Rizza) on Pian Cansiglio, whichprovided the opportunity to conduct tracer tests. Fluorescent dyes were injected in September 2008 in Abisso Col de la Rizza (uranine) and in Bus della Genziana (tinopal CBS-X). Over a period of three months, local cavers conducted an intense sampling programme, whichincluded collecting water samples, charcoal bags and cotton lints. Automated samplers were used for highfrequency monitoring at two of the springs. Tinopal was not detected, so the connection between Bus della Genziana and the springs was not demonstrated. The connection between Abisso Col de la Rizza and two of the springs was demonstrated by uranine. A mean velocity of 248 m/day results from the tracer concentration peaks; intense rainfall events increased the flow velocities four to five times. Different hypotheses are considered in order to explain the low mass recovery rate (32-40% of the injected mass). The uranine tracer test demonstrated that Pian Cansiglio aquifer contributes to the two Livenza springs; it also opens a question about the third spring, whichprobably originates from the Mount Cavallo area (another limestone massif close to Pian Cansiglio). The rapid response to rainfall recharge suggests a vulnerability of the spring system, further supporting the importance of conducting a detailed hydrogeological study.