ArrayQuest: a web resource for the analysis of DNA microarray data

Background  

Numerous microarray analysis programs have been created through the efforts of Open Source software development projects. Providing browser-based interfaces that allow these programs to be executed over the Internet enhances the applicability and utility of these analytic software tools.     

The accuracy of several multiple sequence alignment programs for proteins

Background  

There have been many algorithms and software programs implemented for the inference of multiple sequence alignments of protein and DNA sequences. The "true" alignment is usually unknown due to the incomplete knowledge of the evolutionary history of the sequences, making it difficult to gauge the relative accuracy of the programs.     

RETRACTED ARTICLE: TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics

Background  

Most analysis programs for inferring molecular phylogenies are difficult to use, in particular for researchers with little programming experience.     

Snagger: A user-friendly program for incorporating additional information for tagSNP selection

Background  

There has been considerable effort focused on developing efficient programs for tagging single-nucleotide polymorphisms (SNPs). Many of these programs do not account for potential reduced genomic coverage resulting from genotyping failures nor do they preferentially select SNPs based on functionality, which may be more likely to be biologically important.     

Genome-wide analysis of mRNA decay patterns during early <Emphasis Type="Italic">Drosophila</Emphasis>development

Background  

The modulation of mRNA levels across tissues and time is key for the establishment and operation of the developmental programs that transform the fertilized egg into a fully formed embryo. Although the developmental mechanisms leading to differential mRNA synthesis are heavily investigated, comparatively little attention is given to the processes of mRNA degradation and how these relate to the molecular programs controlling development.     

EzArray: A web-based highly automated Affymetrix expression array data management and analysis system

Background  

Though microarray experiments are very popular in life science research, managing and analyzing microarray data are still challenging tasks for many biologists. Most microarray programs require users to have sophisticated knowledge of mathematics, statistics and computer skills for usage. With accumulating microarray data deposited in public databases, easy-to-use programs to re-analyze previously published microarray data are in high demand.     

Combining gene prediction methods to improve metagenomic gene annotation

Background  

Traditional gene annotation methods rely on characteristics that may not be available in short reads generated from next generation technology, resulting in suboptimal performance for metagenomic (environmental) samples. Therefore, in recent years, new programs have been developed that optimize performance on short reads. In this work, we benchmark three metagenomic gene prediction programs and combine their predictions to improve metagenomic read gene annotation.     

Spatial and temporal investigations of reported movements,births and deaths of cattle and pigs in Sweden

Background  

Livestock movements can affect the spread and control of contagious diseases and new data recording systems enable analysis of these movements. The results can be used for contingency planning, modelling of disease spread and design of disease control programs.     

GPFrontend and GPGraphics: graphical analysis tools for genetic association studies

Background  

Most software packages for whole genome association studies are non-graphical, purely text based programs originally designed to run with UNIX-like operating systems. Graphical output is often not intended or supposed to be performed with other command line tools, e.g. gnuplot.     

Scanning sequences after Gibbs sampling to find multiple occurrences of functional elements

Background  

Many DNA regulatory elements occur as multiple instances within a target promoter. Gibbs sampling programs for finding DNA regulatory elements de novo can be prohibitively slow in locating all instances of such an element in a sequence set.     

Identification of a <Emphasis Type="Italic">Rice stripe necrosis virus</Emphasis> resistance locus and yield component QTLs using <Emphasis Type="Italic">Oryza sativa</Emphasis> × <Emphasis Type="Italic">O. glaberrima</Emphasis> introgression lines

Background  

Developing new population types based on interspecific introgressions has been suggested by several authors to facilitate the discovery of novel allelic sources for traits of agronomic importance. Chromosome segment substitution lines from interspecific crosses represent a powerful and useful genetic resource for QTL detection and breeding programs.     

An innovative approach for testing bioinformatics programs using metamorphic testing

Background  

Recent advances in experimental and computational technologies have fueled the development of many sophisticated bioinformatics programs. The correctness of such programs is crucial as incorrectly computed results may lead to wrong biological conclusion or misguide downstream experimentation. Common software testing procedures involve executing the target program with a set of test inputs and then verifying the correctness of the test outputs. However, due to the complexity of many bioinformatics programs, it is often difficult to verify the correctness of the test outputs. Therefore our ability to perform systematic software testing is greatly hindered.     

Patterns of human gene expression variance show strong associations with signaling network hierarchy

Background  

Understanding organizational principles of cellular networks is one of the central goals of systems biology. Although much has been learnt about gene expression programs under specific conditions, global patterns of expressional variation (EV) of genes and their relationship to cellular functions and physiological responses is poorly understood.     

<Emphasis Type="Italic">ClustalXeed</Emphasis>: a GUI-based grid computation version for high performance and terabyte size multiple sequence alignment

Background  

There is an increasing demand to assemble and align large-scale biological sequence data sets. The commonly used multiple sequence alignment programs are still limited in their ability to handle very large amounts of sequences because the system lacks a scalable high-performance computing (HPC) environment with a greatly extended data storage capacity.     

IRSS: a web-based tool for automatic layout and analysis of IRES secondary structure prediction and searching system in silico

Background  

Internal ribosomal entry sites (IRESs) provide alternative, cap-independent translation initiation sites in eukaryotic cells. IRES elements are important factors in viral genomes and are also useful tools for bi-cistronic expression vectors. Most existing RNA structure prediction programs are unable to deal with IRES elements.     

Studies on <Emphasis Type="Italic">Xenopus laevis</Emphasis>intestine reveal biological pathways underlying vertebrate gut adaptation from embryo to adult

Background  

To adapt to its changing dietary environment, the digestive tract is extensively remodeled from the embryo to the adult during vertebrate development. Xenopus laevis metamorphosis is an excellent model system for studying mammalian gastrointestinal development and is used to determine the genes and signaling programs essential for intestinal development and maturation.