Applications of next-generation sequencing technologies and computational tools in molecular evolution and aquatic animals conservation studies : a short review

Aquatic ecosystems that form major biodiversity hotspots are critically threatened due to environmental and anthropogenic stressors. We believe that, in this genomic era, computational methods can be applied to promote aquatic biodiversity conservation by addressing questions related to the evolutionary history of aquatic organisms at the molecular level. However, huge amounts of genomics data generated can only be discerned through the use of bioinformatics. Here, we examine the applications of next-generation sequencing technologies and bioinformatics tools to study the molecular evolution of aquatic animals and discuss the current challenges and future perspectives of using bioinformatics toward aquatic animal conservation efforts

XML in Motion from Genome to Drug

Information technology (IT) has emerged as a central to the solution of contemporary genomics and drug discovery problems. Researchers involved in genomics, proteomics, transcriptional profiling, high throughput structure determination, and in other sub-disciplines of bioinformatics have direct impact on this IT revolution. As the full genome sequences of many species, data from structural genomics, micro-arrays, and proteomics became available, integration of these data to a common platform require sophisticated bioinformatics tools. Organizing these data into knowledgeable databases and developing appropriate software tools for analyzing the same are going to be major challenges. XML (eXtensible Markup Language) forms the backbone of biological data representation and exchange over the internet, enabling researchers to aggregate data from various heterogeneous data resources. The present article covers a comprehensive idea of the integration of XML on particular type of biological databases mainly dealing with sequence-structure-function relationship and its application towards drug discovery. This e-medical science approach should be applied to other scientific domains and the latest trend in semantic web applications is also highlighted

Current status and future perspectives of bioinformatics in Tanzania

The main bottleneck in advancing genomics in present times is the lack of expertise in using bioinformatics tools and approaches for data mining in raw DNA sequences generated by modern high throughput technologies such as next generation sequencing. Although bioinformatics has been making major progress and contributing to the development in the rest of the world, it has still not yet fully integrated the tertiary education and research sector in Tanzania. This review aims to introduce a summary of recent achievements, trends and success stories of application of bioinformatics in biotechnology. The applications of bioinformatics in the fields such as molecular biology, biotechnology, medicine and agriculture, the global trend of bioinformatics, accessibility bioinformatics products in Tanzania, bioinformatics training initiatives in Tanzania, the future prospects of bioinformatics use in biotechnology globally and Tanzania in particular are reviewed. The paper is of interest and importance to rouse public awareness of the new opportunities that could be brought about by bioinformatics to address many research problems relevant to Tanzania and sub-Sahara Africa.Keywords: Bioinformatics, Biotechnology, Genomics, Tanzania

Bioinformatics tools for analysing viral genomic data

The field of viral genomics and bioinformatics is experiencing a strong resurgence due to high-throughput sequencing (HTS) technology, which enables the rapid and cost-effective sequencing and subsequent assembly of large numbers of viral genomes. In addition, the unprecedented power of HTS technologies has enabled the analysis of intra-host viral diversity and quasispecies dynamics in relation to important biological questions on viral transmission, vaccine resistance and host jumping. HTS also enables the rapid identification of both known and potentially new viruses from field and clinical samples, thus adding new tools to the fields of viral discovery and metagenomics. Bioinformatics has been central to the rise of HTS applications because new algorithms and software tools are continually needed to process and analyse the large, complex datasets generated in this rapidly evolving area. In this paper, the authors give a brief overview of the main bioinformatics tools available for viral genomic research, with a particular emphasis on HTS technologies and their main applications. They summarise the major steps in various HTS analyses, starting with quality control of raw reads and encompassing activities ranging from consensus and de novo genome assembly to variant calling and metagenomics, as well as RNA sequencing

Functional genomics in forage and turf - present status and future prospects

The recent advances in plant genomics have greatly influenced basic research in many agriculturally important crops. Along with the availability of complete genome information from the model grass species rice and the model legume species M. trucncatula, the functional genomics activities in other crop species will accelerate the genomics studies of forage and turf. Brachypodium distachyon was recently proposed as a new model plant for forage and turf grass genomics studies. The combination of bioinformatics and genomics will enhance our understanding of the molecular functions of forage and turf species. This review focuses on recent advances and applications of functional genomics for large-scale EST projects, global gene expression analyses, proteomics, and metabolic profiling, as well as the impact of functional genomics on improvement of forage and turf crops. Key words: Functional genomics, forage and turf grasses, ESTs, microarray, proteomics, metabolomics, Medicago truncatula, legume. African Journal of Biotechnology Vol. 2 (12), pp. 521-527, December 200

The 20th anniversary of EMBnet: 20 years of bioinformatics for the Life Sciences community

The EMBnet Conference 2008, focusing on 'Leading Applications and Technologies in Bioinformatics', was organized by the European Molecular Biology network (EMBnet) to celebrate its 20th anniversary. Since its foundation in 1988, EMBnet has been working to promote collaborative development of bioinformatics services and tools to serve the European community of molecular biology laboratories. This conference was the first meeting organized by the network that was open to the international scientific community outside EMBnet. The conference covered a broad range of research topics in bioinformatics with a main focus on new achievements and trends in emerging technologies supporting genomics, transcriptomics and proteomics analyses such as high-throughput sequencing and data managing, text and data-mining, ontologies and Grid technologies. Papers selected for publication, in this supplement to BMC Bioinformatics, cover a broad range of the topics treated, providing also an overview of the main bioinformatics research fields that the EMBnet community is involved in

Current Status and Future Perspectives of Bioinformatics in Tanzania

The main bottleneck in advancing genomics in present times is the lack of expertise in using bioinformatics tools and approaches for data mining in raw DNA sequences generated by modern high throughput technologies such as next generation sequencing. Although bioinformatics has been making major progress and contributing to the development in the rest of the world, it has still not yet fully integrated the tertiary education and research sector in Tanzania. This review aims to introduce a summary of recent achievements, trends and success stories of application of bioinformatics in biotechnology. The applications of bioinformatics in the fields such as molecular biology, biotechnology, medicine and agriculture, the global trend of bioinformatics, accessibility bioinformatics products in Tanzania, bioinformatics training initiatives in Tanzania, the future prospects of bioinformatics use in biotechnology globally and Tanzania in particular are reviewed. The paper is of interest and importance to rouse public awareness of the new opportunities that could be brought about by bioinformatics to address many research problems relevant to Tanzania and sub-Sahara Africa

Bioinformatics and Next Generation Sequencing: Applications of Arthropod Genomes

Over the past decade, the Next Generation Sequencing (NGS) technology has been broadly applied in many areas such as genomics, medical diagnosis, biotechnology, virology, biological systematics, forensic biology, and anthropology. Taken together, it has offered us brilliant insights into life sciences. Most of the work presented in this thesis describes NGS applications on genome assembly, genome annotation, and comparative genomics, using arthropods as case studies: (1) by sequencing and analyzing the genomes of three Tetranychus spider mites with three completely different feeding behaviors, we uncovered genomic signature variations and indicative of pest adaptations; (2) we sequenced, assembled and annotated five Brevipalpus flat mite genomes and their corresponding endosymbiont Cardinium genomes. Comparative genomics reveals herbivorous pest adaptations and parthenogenesis; (3) the complete genomic analysis of parasitoid wasp Copidosoma floridanum indicates the mechanism of polyembryony of such primary parasite of moths. By bioinformatics and genomics approaches, my study provides the genomic basis and establishes the hypotheses for the future biology in pest and arthropod researches. These NGS applications of arthropod genomes will offer new insights into arthropod evolution and plant-herbivore interactions, open unique opportunities to develop novel plant protection strategies, and additionally, provide arthropod genomic resources as well