fastQ_brew: module for analysis, preprocessing, and reformatting of FASTQ sequence data

Abstract Background Next generation sequencing datasets are stored as FASTQ formatted files. In order to avoid downstream artefacts, it is critical to implement a robust preprocessing protocol of the FASTQ sequence in order to determine the integrity and quality of the data. Results Here I describe fastQ_brew which is a package that provides a suite of methods to evaluate sequence data in FASTQ format and efficiently implements a variety of manipulations to filter sequence data by size, quality and/or sequence. fastQ_brew allows for mismatch searches to adapter sequences, left and right end trimming, removal of duplicate reads, as well as reads containing non-designated bases. fastQ_brew also returns summary statistics on the unfiltered and filtered FASTQ data, and offers FASTQ to FASTA conversion as well as FASTQ reverse complement and DNA to RNA manipulations. Conclusions fastQ_brew is open source and freely available to all users at the following webpage: https://github.com/dohalloran/fastQ_brew

Summary of <i>phylo-node</i> applications.

<p>Summary of <i>phylo-node</i> applications.</p

Workflow for <i>phylo-node</i>.

<p>phylo-node is organized into a workflow of connected modules and application scripts. In order to interface with a software tool, the base wrapper module is invoked to process command-line requests that are then passed into the software specific module. The input for the specific software can be passed into the base wrapper from a folder specified by the user or by using the sequence retrieval module which is contained within the <i>Sequence</i> directory. The <i>Pipes</i> directory contains a module for easy piping of data between applications while binaries and executables can be downloaded using the <i>get_executable</i> module from within the <i>Download</i> folder to deploy software specific modules within the <i>Run</i> directory or to provide applications to a web server from within the <i>Server</i> directory.</p

NCX-DB: a unified resource for integrative analysis of the sodium calcium exchanger super-family

Abstract Na+/Ca2+ exchangers are low-affinity high-capacity transporters that mediate Ca2+ extrusion by coupling Ca2+ efflux to the influx of Na+ ions. The Na+/Ca2+ exchangers form a super-family comprised of three branches each differing in ion-substrate selectivity: Na+/Ca2+ exchangers (NCX), Na+/Ca2+/K+ exchangers, and Ca2+/cation exchangers. Their primary function is to maintain Ca2+ homeostasis and play a particularly important role in excitable cells that experience transient Ca2+ fluxes. Research into the role and activity of Na+/Ca2+ exchangers has focused extensively on the cardio-vascular system, however, growing evidence suggests that Na+/Ca2+ exchangers play a key role in neuronal processes such as memory formation, learning, oligodendrocyte differentiation, neuroprotection during brain ischemia and axon guidance. They have also been implicated in pathologies such as Alzheimer’s disease, Parkinson’s disease, Multiple Sclerosis and Epilepsy, however, a clear understanding of their mechanism during disease is lacking. To date, there has never been a central resource or database for Na+/Ca2+ exchangers. With clear disease relevance and ever-increasing research on Na+/Ca2+ exchangers from both model and non-model species, a database that unifies the data on Na+/Ca2+ exchangers is needed for future research. NCX-DB is a publicly available database with a web interface that enables users to explore various Na+/Ca2+ exchangers, perform cross-species sequence comparison, identify new exchangers, and stay-up to date with recent literature. NCX-DB is available on the web via an interactive user interface with an intuitive design, which is applicable for the identification and comparison of Na+/Ca2+ exchanger proteins across diverse species