EMBLmyGFF3: a converter facilitating genome annotation submission to European Nucleotide Archive.

Objective: The state-of-the-art genome annotation tools output GFF3 format files, while this format is not accepted as submission format by the International Nucleotide Sequence Database Collaboration (INSDC) databases. Converting the GFF3 format to a format accepted by one of the three INSDC databases is a key step in the achievement of genome annotation projects. However, the flexibility existing in the GFF3 format makes this conversion task difficult to perform.

MetLab: An In Silico Experimental Design, Simulation and Analysis Tool for Viral Metagenomics Studies.

Metagenomics, the sequence characterization of all genomes within a sample, is widely used as a virus discovery tool as well as a tool to study viral diversity of animals. Metagenomics can be considered to have three main steps; sample collection and preparation, sequencing and finally bioinformatics. Bioinformatic analysis of metagenomic datasets is in itself a complex process, involving few standardized methodologies, thereby hampering comparison of metagenomics studies between research groups.

The genomes of three stocks comprising the most widely utilized live sporozoite Theileria parva vaccine exhibit very different degrees and patterns of sequence divergence.

Background: There are no commercially available vaccines against human protozoan parasitic diseases, despite the success of vaccination-induced long-term protection against infectious diseases. East Coast fever, caused by the protist Theileria parva, kills one million cattle each year in sub-Saharan Africa, and contributes significantly to hunger and poverty in the region. A highly effective, live, multi-isolate vaccine against T.

Web-based biobank system infrastructure monitoring using Python, Perl, and PHP.

The establishment and maintenance of biobanks is only as worthwhile as the security and logging of the biobank contents. We have designed a monitoring system that continuously measures temperature and gas content, records the movement of samples in and out of the biobank, and also records the opening and closing of the freezers-storing the results and images in a database. We have also incorporated an early warning feature that sends out alerts, via SMS and email, to responsible persons if any measurement is recorded outside the acceptable limits, guaranteeing the integrity of biobanked samples, as well as reagents used in sample analysis.

Viral metagenomics demonstrates that domestic pigs are a potential reservoir for Ndumu virus.

Background: The rising demand for pork has resulted in a massive expansion of pig production in Uganda. This has resulted in increased contact between humans and pigs. Pigs can act as reservoirs for emerging infectious diseases.

Comprehensive human urine standards for comparability and standardization in clinical proteome analysis.

Purpose: Urine proteomics is emerging as a powerful tool for biomarker discovery. The purpose of this study is the development of a well-characterized "real life" sample that can be used as reference standard in urine clinical proteomics studies.

Experimental Design: We report on the generation of male and female urine samples that are extensively characterized by different platforms and methods (CE-MS, LC-MS, LC-MS/MS, 1-D gel analysis in combination with nano-LC MS/MS (using LTQ-FT ultra), and 2-DE-MS) for their proteome and peptidome.