Springer protocols feed by Bioinformatics 
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This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.e-DNA Meta-Barcoding: From NGS Raw Data to Taxonomic Profiling
In recent years, thanks to the essential support provided by the Next-Generation Sequencing (NGS) technologies, Metagenomics is enabling the direct access to the taxonomic and functional composition of mixed microbial communities living in any environmental niche, without the prerequisite to isolate or culture the single organisms. This approach has already been successfully applied for the analysis of many habitats, such as water or soil natural environments, also characterized by extreme physical and chemical conditions, food supply chains, and animal organisms, including humans. A shotgun sequencing approach can lead to...
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
NGS-Trex: An Automatic Analysis Workflow for RNA-Seq Data
RNA-Seq technology allows the rapid analysis of whole transcriptomes taking advantage of next-generation sequencing platforms. Moreover with the constant decrease of the cost of NGS analysis RNA-Seq is becoming very popular and widespread. Unfortunately data analysis is quite demanding in terms of bioinformatic skills and infrastructures required, thus limiting the potential users of this method. (Source: Springer protocols feed by Bioinformatics)
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
Using Deep Sequencing Data for Identification of Editing Sites in Mature miRNAs
Deep sequencing has many possible applications; one of them is the identification and quantification of RNA editing sites. The most common type of RNA editing is adenosine to inosine (A-to-I) editing. A prerequisite for this editing process is a double-stranded RNA (dsRNA) structure. Such dsRNAs are formed as part of the microRNA (miRNA) maturation process, and it is therefore expected that miRNAs are affected by A-to-I editing. Indeed, tens of editing sites were found in miRNAs, some of which change the miRNA binding specificity. Here, we describe a protocol for the identification of RNA editing sites in mature miRNAs usi...
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
Prediction of miRNA Targets
Computational methods for miRNA target prediction are currently undergoing extensive review and evaluation. There is still a great need for improvement of these tools and bioinformatics approaches are looking towards high-throughput experiments in order to validate predictions. The combination of large-scale techniques with computational tools will not only provide greater credence to computational predictions but also lead to the better understanding of specific biological questions. Current miRNA target prediction tools utilize probabilistic learning algorithms, machine learning methods and even empirical biologically de...
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
Detection of Post-Transcriptional RNA Editing Events
The advent of deep sequencing technologies has greatly improved the study of complex eukaryotic genomes and transcriptomes, providing the unique opportunity to investigate posttranscriptional molecular mechanisms as alternative splicing and RNA editing at single base-pair resolution. RNA editing by adenosine deamination (A-to-I) is widespread in humans and can lead to a variety of biological effects depending on the RNA type or the RNA region involved in the editing modification. (Source: Springer protocols feed by Bioinformatics)
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
Transcriptome Assembly and Alternative Splicing Analysis
Alternative Splicing (AS) is the molecular phenomenon whereby multiple transcripts are produced from the same gene locus. As a consequence, it is responsible for the expansion of eukaryotic transcriptomes. Aberrant AS is involved in the onset and progression of several human diseases. Therefore, the characterization of exon–intron structure of a gene and the detection of corresponding transcript isoforms is an extremely relevant biological task. Nonetheless, the computational prediction of AS events and the repertoire of alternative transcripts is yet a challenging issue. (Source: Springer protocols feed by Bioinformatics)
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
Quantifying Entire Transcriptomes by Aligned RNA-Seq Data
Massive Parallel Sequencing methods (MPS) can extend and improve the knowledge obtained by conventional microarray technology, both for mRNAs and noncoding RNAs. Although RNA quality and library preparation protocols are the main source of variability, the bioinformatics pipelines for RNA-seq data analysis are very complex and the choice of different tools at each stage of the analysis can significantly affect the overall results. In this chapter we describe the pipelines we use to detect miRNA and mRNA differential expression. (Source: Springer protocols feed by Bioinformatics)
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
Fast Prediction of RNA–RNA Interaction Using Heuristic Algorithm
We describe the algorithm’s concurrency and parallelism for a multicore chip. The proposed algorithm has been performed on some datasets including CopA-CopT, R1inv-R2inv, Tar-Tar*, DIS-DIS, and IncRNA54-RepZ in Escherichia coli bacteria. The method has high validity and efficiency, and it is run in low computational time in comparison to other approaches. (Source: Springer protocols feed by Bioinformatics)
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
Modeling and Predicting RNA Three-Dimensional Structures
Modeling the three-dimensional structure of RNAs is a milestone toward better understanding and prediction of nucleic acids molecular functions. Physics-based approaches and molecular dynamics simulations are not tractable on large molecules with all-atom models. To address this issue, coarse-grained models of RNA three-dimensional structures have been developed. In this chapter, we describe a graphical modeling based on the Leontis–Westhof extended base-pair classification. This representation of RNA structures enables us to identify highly conserved structural motifs with complex nucleotide interactions in structur...
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
Drawing and Editing the Secondary Structure(s) of RNA
We describe the file formats and structural descriptions accepted by popular RNA visualization tools. We also provide command lines and Python scripts to ease the user’s access to advanced features. Finally, we discuss and illustrate alternative approaches to visualize the secondary structure in the presence of probing data, pseudoknots, RNA–RNA interactions, and comparative data. (Source: Springer protocols feed by Bioinformatics)
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
De Novo Secondary Structure Motif Discovery Using RNAProfile
We describe here how conserved secondary structure motifs shared by functionally related RNA sequences can be detected through the software tool RNAProfile. RNAProfile takes as input a set of unaligned RNA sequences expected to share a common motif, and outputs the regions that are most conserved throughout the sequences, according to a similarity measure that takes into account both the sequence of the regions and the secondary structure they can form according to base-pairing and thermodynamic rules. (Source: Springer protocols feed by Bioinformatics)
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
A Simple Protocol for the Inference of RNA Global Pairwise Alignments
In conclusion, the proposed workflow for pairwise RNA alignment depends on the input RNA primary sequence identity and the availability of reliable secondary structures. (Source: Springer protocols feed by Bioinformatics)
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
RNA Secondary Structure Prediction from Multi-Aligned Sequences
It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from evolutionarily related sequences is one important task in RNA bioinformatics; the methods are useful not only to further functional analyses of ncRNAs but also to improve the accuracy of secondary structure predictions and to find novel functional RNAs from the genome. In this review, I focus on common secondary structure prediction from a given aligned RNA sequence, in which one secondary s...
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
Free Energy Minimization to Predict RNA Secondary Structures and Computational RNA Design
Determining the RNA secondary structure from sequence data by computational predictions is a long-standing problem. Its solution has been approached in two distinctive ways. If a multiple sequence alignment of a collection of homologous sequences is available, the comparative method uses phylogeny to determine conserved base pairs that are more likely to form as a result of billions of years of evolution than by chance. In the case of single sequences, recursive algorithms that compute free energy structures by using empirically derived energy parameters have been developed. This latter approach of RNA folding prediction b...
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
Mining the Electronic Health Record for Disease Knowledge
The growing amount and availability of electronic health record (EHR) data present enhanced opportunities for discovering new knowledge about diseases. In the past decade, there has been an increasing number of data and text mining studies focused on the identification of disease associations (e.g., disease–disease, disease–drug, and disease–gene) in structured and unstructured EHR data. This chapter presents a knowledge discovery framework for mining the EHR for disease knowledge and describes each step for data selection, preprocessing, transformation, data mining, and interpretation/validation. Topics ...
Source: Springer protocols feed by Bioinformatics - May 2, 2014 Category: Bioinformatics Source Type: news
