Bioinformatics tools and databases for analysis of next-generation sequence data

Genome sequencing has been revolutionized by next-generation technologies, which can rapidly produce vast quantities of data at relatively low cost. With data production now no longer being limited, there is a huge challenge to analyse the data flood and interpret biological meaning. Bioinformatics scientists have risen to the challenge and a large number of software tools and databases have been produced and these continue to evolve with this rapidly advancing field. Here, we outline some of the tools and databases commonly used for the analysis of next-generation sequence data with comment on their utility.     

Bioinformatics approaches and resources for single nucleotide polymorphism functional analysis

Since the initial sequencing of the human genome, many projects are underway to understand the effects of genetic variation between individuals. Predicting and understanding the downstream effects of genetic variation using computational methods are becoming increasingly important for single nucleotide polymorphism (SNP) selection in genetics studies and understanding the molecular basis of disease. According to the NIH, there are now more than four million validated SNPs in the human genome. The volume of known genetic variations lends itself well to an informatics approach. Bioinformaticians have become very good at functional inference methods derived from functional and structural genomics. This review will present a broad overview of the tools and resources available to collect and understand functional variation from the perspective of structure, expression, evolution and phenotype. Additionally, public resources available for SNP identification and characterisation are summarised.     

Bioinformatics databases and tools in virology research: an overview

Viruses are major factors of human infectious diseases. Understanding of the structure-function correlation in viruses is important for the identification of potential anti-viral inhibitors and vaccine targets. In virology research, virus-related databases and bioinformatic analysis tools are essential for discerning relationships within complex datasets about viruses and host-virus interactions. Bioinformatic analyses on viruses include the identification of open reading frames, gene prediction, homology searching, sequence alignment, and motif and epitope recognition. The predictions of features such as transmembrane domains, glycosylation sites, and protein secondary and tertiary structure are important for analyzing the structure-function relationship of proteins encoded in viral genomes. Biochemical pathway analysis can help elucidate information at the biological systems level. Microarray analysis provides methods for high throughput screening and gene expression profiling. Virus-related bioinformatics databases include those concerned with viral sequences, taxonomy, homologous protein families, structures, or dedicated to specific viruses such as influenza and herpes simplex virus (HSV). This review provides a guide and overview of computational programs for these analyses as a resource for genomics and proteomics studies in virology research. These resources are useful for understanding viral diseases, as well as for the design and development of anti-viral agents.     

Molecular genetic tools in Toxoplasma and Plasmodium: achievements and future needs

The recent awarding of the Nobel prize to Andrew Fire and Craig Mello for the discovery of RNA-interference (RNAi) in plants once more demonstrated the importance of basic science in understanding biological mechanisms. Importantly, this discovery led to the establishment of powerful approaches to study gene function in a wide array of organisms. While a robust RNAi-technology remains elusive in apicomplexan parasites, other molecular genetic technologies have been introduced in recent years. Now, in the post genomic era, the task is to apply these methods to validate and functionally dissect an ever-expanding list of putative vaccine and drug candidates. The ultimate aim of such studies is to transform our knowledge of the genome to the knowledge of the phenome and ultimately new intervention strategies in these important pathogenic organisms. However, substantial limitations remain to the current repertoire of available molecular tools, which limits a comprehensive analysis of these candidates, especially of essential genes. This review summarises the methodologies available for functional gene analysis in apicomplexan parasites and discusses further needs in tool development.     

Integration of tools and resources for display and analysis of genomic data for protozoan parasites

Centralisation of tools for analysis of genomic data is paramount in ensuring that research is always carried out on the latest currently available data. As such, World Wide Web sites providing a range of online analyses and displays of data can play a crucial role in guaranteeing consistency of in silico work. In this respect, the protozoan parasite research community is served by several resources, either focussing on data and tools for one species or taking a broader view and providing tools for analysis of data from many species, thereby facilitating comparative studies. In this paper, we give a broad overview of the online resources available. We then focus on the GeneDB project, detailing the features and tools currently available through it. Finally, we discuss data curation and its importance in keeping genomic data 'relevant' to the research community.     

Atlas of genetics and cytogenetics in oncology and haematology, an interactive database

The 'Atlas of Genetics and Cytogenetics in Oncology and Haematology' (http://www.infobiogen.fr/services/chromcancer ) is a database devoted to chromosome abnormalities in cancer, cancer-prone diseases and genes involved in cancer. Information presented in each page is concise and updated. This database is made for and by: cytogeneticists, molecular biologists, clinicians in oncology and in haematology, and pathologists, who are encouraged to contribute.     

Performance comparison and evaluation of software tools for microRNA deep-sequencing data analysis

With the development of next-generation sequencing (NGS) techniques, many software tools have emerged for the discovery of novel microRNAs (miRNAs) and for analyzing the miRNAs expression profiles. An overall evaluation of these diverse software tools is lacking. In this study, we evaluated eight software tools based on their common feature and key algorithms. Three deep-sequencing data sets were collected from different species and used to assess the computational time, sensitivity and accuracy of detecting known miRNAs as well as their capacity for predicting novel miRNAs. Our results provide useful information for researchers to facilitate their selection of the optimal software tools for miRNA analysis depending on their specific requirements, i.e. novel miRNAs discovery or miRNA expression profile analysis of sequencing data sets.     

Transposable elements as tools for genomics and genetics in Drosophila.

The P-element has been the workhorse of Drosophila genetics since it was developed as a tool for transgenesis in 1982; the subsequent development of a variety of systems based on the transposon have provided a range of powerful and flexible tools for genetics and genomics applications. P-element insertions are frequently used as starting-points for generating chromosomal deletions to remove flanking genes, either by screening for imprecise excision events or by selecting for male recombination events. Elements that utilise the yeast FLP/FLP recombination target (FRT) site-specific recombination system have been widely used to generate molecularly marked mitotic clones for mosaic analysis, extending the reach of this powerful genetic tool to virtually all areas of developmental biology. P-elements are still widely used as traditional mutagenesis reagents and form the backbone of projects aimed at generating insertions in every predicted gene in the fly genome. In addition, vectors based on the FLP/FRT system are being used for genome-wide applications, including the development of molecularly-mapped deletion and duplication kits. In addition to these 'traditional' genetic approaches, a variety of engineered elements have been developed for a wide range of transgenic applications, including enhancer trapping, gene-tagging, targeted misexpression, RNA interference (RNAi) delivery and homologous recombination/gene replacement. To complement the use of P-elements, alternative transposon vectors have been developed. The most widely used of these are the lepidopteran element piggyBac and a Drosophila hydei transposon, Minos. In total, a range of transposon vectors offers the Drosophila biologist considerable flexibility and sophistication in manipulating the genome of the fly and has allowed rapid advances in all areas of developmental biology and genome science.     

An integrated Arabidopsis annotation database for Affymetrix Genechip data analysis, and tools for regulatory motif searches

Genome-scale sequencing projects have provided the essential information required for the construction of entire genome chips or microarrays for RNA expression studies. The Arabidopsis and rice genomes have been sequenced and whole-genome oligonucleotide arrays are being manufactured. These should soon become available to researchers. Expression studies using genomic-scale expression arrays are providing us with a vast quantity of information at a rapid pace. The rate-limiting step in this type of experiments is not the data generation step but rather the data analysis component of experiments. We report improvements that should facilitate the analysis of Affymetrix Genechip expression data.     

AllergenPro: an integrated database for allergenicity analysis and prediction

The National Agricultural Biotechnology Information Center (NABIC) reconstructed an AllergenPro database for allergenic proteins analysis and allergenicity prediction. The AllergenPro is an integrated web-based system providing information about allergen in foods, microorganisms, animals and plants. The allergen database has the three main features namely, (1) allergen list with epitopes, (2) searching of allergen using keyword, and (3) methods for allergenicity prediction. This updated AllergenPro outputs the search based allergen information through a user-friendly web interface, and users can run tools for allergenicity prediction using three different methods namely, (1) FAO/WHO, (2) motif-based and (3) epitope-based methods.

Availability

The database is available for free at http://nabic.rda.go.kr/allergen/     

An applications-focused review of comparative genomics tools: capabilities,limitations and future challenges

A team at the Lawrence Livermore National Laboratory (LLNL) was given the task of using computational tools to speed up the development of DNA diagnostics for pathogen detection. This work will be described in another paper in this issue (see pages 133-149). To achieve this goal it was necessary to understand the merits and limitations of the various available comparative genomics tools. A review of some recent tools for multisequence/genome alignment and substring comparison is presented, within the general framework of applicability to a large-scale application. We note that genome alignments are important for many things, only one of which is pathogen detection. Understanding gene function, gene regulation, gene networks, phylogenetic studies and other aspects of evolution all depend on accurate nucleic acid and protein sequence alignment. Selecting appropriate tools can make a large difference in the quality of results obtained and the effort required.