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
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
Deciphering Metatranscriptomic Data
Metatranscriptomic data contributes another piece of the puzzle to understanding the phylogenetic structure and function of a community of organisms. High-quality total RNA is a bountiful mixture of ribosomal, transfer, messenger and other noncoding RNAs, where each family of RNA is vital to answering questions concerning the hidden microbial world. Software tools designed for deciphering metatranscriptomic data fall under two main categories: the first is to reassemble millions of short nucleotide fragments produced by high-throughput sequencing technologies into the original full-length transcriptomes for all organisms w...
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
Computational Design of Artificial RNA Molecules for Gene Regulation
RNA interference (RNAi) is a powerful tool for the regulation of gene expression. Small exogenous noncoding RNAs (ncRNAs) such as siRNA and shRNA are the active silencing agents, intended to target and cleave complementary mRNAs in a specific way. They are widely and successfully employed in functional studies, and several ongoing and already completed siRNA-based clinical trials suggest encouraging results in the regulation of overexpressed genes in disease. (Source: Springer protocols feed by Bioinformatics)
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
Analysis of Alternative Splicing Events in Custom Gene Datasets by AStalavista
Alternative splicing (AS) is a eukaryotic principle to derive more than one RNA product from transcribed genes by removing distinct subsets of introns from a premature polymer. We know today that this process is highly regulated and makes up a large part of the differences between species, cell types, and states. The key to compare AS across different genes or organisms is to tokenize the AS phenomenon into atomary units, so-called AS events. These events then usually are grouped by common patterns to investigate the underlying molecular mechanisms that drive their regulation. However, attempts to decompose loci with AS ob...
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
ASPicDB: A Database Web Tool for Alternative Splicing Analysis
Alternative splicing (AS) is a basic molecular phenomenon that increases the functional complexity of higher eukaryotic transcriptomes. Indeed, through AS individual gene loci can generate multiple RNAs from the same pre-mRNA. AS has been investigated in a variety of clinical and pathological studies, such as the transcriptome regulation in cancer. In human, recent works based on massive RNA sequencing indicate that >95 % of pre-mRNAs are processed to yield multiple transcripts. Given the biological relevance of AS, several computational efforts have been done leading to the implementation of novel algorithms and specif...
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
Rfam: Annotating Families of Non-Coding RNA Sequences
The primary task of the Rfam database is to collate experimentally validated noncoding RNA (ncRNA) sequences from the published literature and facilitate the prediction and annotation of new homologues in novel nucleotide sequences. We group homologous ncRNA sequences into “families” and related families are further grouped into “clans.” We collate and manually curate data cross-references for these families from other databases and external resources. Our Web site offers researchers a simple interface to Rfam and provides tools with which to annotate their own sequences using our covariance models ...
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
A Guideline for the Annotation of UTR Regulatory Elements in the UTRsite Collection
Gene expression regulatory elements are scattered in gene promoters and pre-mRNAs. In particular, RNA elements lying in untranslated regions (5′ and 3′UTRs) are poorly studied because of their peculiar features (i.e., a combination of primary and secondary structure elements) which also pose remarkable computational challenges. Several years ago, we began collecting experimentally characterized UTR regulatory elements, developing the specialized database UTRsite. This paper describes the detailed guidelines to annotate cis-regulatory elements in 5′ and 3′ UnTranslated Regions (UTRs) by computational...
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
Exploring the RNA Editing Potential of RNA-Seq Data by ExpEdit
Revealing the impact of A-to-I RNA editing in RNA-Seq experiments is relevant in humans because RNA editing can influence gene expression. In addition, its deregulation has been linked to a variety of human diseases. Exploiting the RNA editing potential in complete RNA-Seq datasets, however, is a challenging task. Indeed, no dedicated software is available, and sometimes deep computational skills and appropriate hardware resources are required. To explore the impact of known RNA editing events in massive transcriptome sequencing experiments, we developed the ExpEdit web service application. In the present work, we provide ...
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
The ViennaRNA Web Services
The ViennaRNA package is a widely used collection of programs for thermodynamic RNA secondary structure prediction. Over the years, many additional tools have been developed building on the core programs of the package to also address issues related to noncoding RNA detection, RNA folding kinetics, or efficient sequence design considering RNA-RNA hybridizations. The ViennaRNA web services provide easy and user-friendly web access to these tools. This chapter describes how to use this online platform to perform tasks such as prediction of minimum free energy structures, prediction of RNA-RNA hybrids, or noncoding RNA detect...
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
Accurate Mapping of RNA-Seq Data
The mapping of RNA-Seq data on genome is not the same as DNA-Seq data, because the junction reads span two exons and have no identical matches at reference genome. In this chapter, we describe a junction read aligner SpliceMap that is based on an algorithm of “half-read seeding” and “seeding extension.” Four analysis steps are integrated in SpliceMap (half-read mapping, seeding selection, seeding extension and junction search, and paired-end filtering), and all toning parameters of these steps can be editable in a single configuration file. Thus, SpliceMap can be executed by a single command. While ...
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
Quality Control of RNA-Seq Experiments
Direct sequencing of the complementary DNA (cDNA) using high-throughput sequencing technologies (RNA-seq) is widely used and allows for more comprehensive understanding of the transcriptome than microarray. In theory, RNA-seq should be able to precisely identify and quantify all RNA species, small or large, at low or high abundance. However, RNA-seq is a complicated, multistep process involving reverse transcription, amplification, fragmentation, purification, adaptor ligation, and sequencing. Improper operations at any of these steps could make biased or even unusable data. Additionally, RNA-seq intrinsic biases (such as ...
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
RIP-Seq Data Analysis to Determine RNA–Protein Associations
Next-generation sequencing (NGS) technologies have opened new avenues of unprecedented power for research in molecular biology and genetics. In particular, their application to the study of RNA-binding proteins (RBPs), extracted through immunoprecipitation (RIP), permits to sequence and characterize all RNAs that were found to be bound in vivo by a given RBP (RIP-Seq). On the other hand, NGS-based experiments, including RIP-Seq, produce millions of short sequence fragments that have to be processed with suitable bioinformatic tools and methods to recover and/or quantify the original sequence sample. In this chapter we prov...
Source: Springer protocols feed by Bioinformatics - January 1, 2015 Category: Bioinformatics Source Type: news
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
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
