Description: This article discusses using WebGBrowse to visualize genome annotation on GBrowse. Although GBrowse is popular for visualizing genomic features along a reference sequence, its installation and configuration are difficult for many biologists. WebGBrowse is a web server that takes a user-supplied annotation file, guides users to configure the display of each genomic feature, and allows users to visualize the genome annotation with integrated GBrowse software. This protocol guides the user through each step of using WebGBrowse.

Description: This article discusses Tracembler. Background: Whole genome shotgun produces increasingly higher coverage of a genome with random sequence reads. Progressive whole genome assembly and eventual finishing sequencing is a process that typically takes several years for large eukaryotic genomes. In the interim, all sequence reads of public sequencing projects are made available in repositories such as the NCBI Trace Archive. For a particular locus, sequencing coverage may be high enough early on to produce a reliable local genome assembly. The authors have developed software, Tracembler, that facilitates in silico chromosome walking by recursively assembling reads of a selected species from the NCBI Trace Archive starting with reads that significantly match sequence seeds supplied by the user. Results: Tracembler takes one or multiple DNA or protein sequence(s) as input to the NCBI Trace Archive BLAST engine to identify matching sequence reads from a species of interest. The BLAST searches are carried out recursively such that BLAST matching sequences identified in previous rounds of searches are used as new queries in subsequent rounds of BLAST searches. The recursive BLAST search stops when either no more new matching sequences are found, a given maximal number of queries is exhausted, or a specified maximum ...

Description: This paper discusses expressed sequence tag sequencing over grid and cloud computing clusters. Abstract: Computer-intensive biological applications are heavily reliant on the availability of computing resources. Grid based HPC clusters and emerging Cloud computing clusters provide a large scale computing environment for scientific users. However, large scale biological application often involves various types of computational tasks which can benefit from different types of computing clusters. Therefore, a high level job scheduling environment which integrates the Grid style HPC clusters and the Cloud computing clusters and manages jobs accordingly based on the characteristics of the jobs is required. In this paper, the authors propose a Web service framework for high-level job scheduling - Swarm. Swarm is developed for scientific applications that must submit massive number of high-throughput jobs or workflows to highly distributed computing clusters. Swarm allows the users to submit jobs to both Grid HPC and Cloud computing clusters. The Swarm service itself is designed to be extensible, lightweight, and easily installable on a desktop or a small server. As a Web service, derivative services based on Swarm can be straightforwardly integrated with Web portals and science gateways. This paper provides the motivation for this research, the architecture of the ...

Description: This article discusses GSV, a web-based genome synteny viewer for customized data. Abstract: Background: The analysis of genome synteny is a common practice in comparative genomics. With the advent of DNA sequencing technologies, individual biologists can rapidly produce their genomic sequences of interest. Although web-based synteny visualization tools are convenient for biologists to use, none of the existing ones allow biologists to upload their own data for analysis. Results: The authors have developed the web-based Genome Synteny Viewer (GSV) that allows users to upload two data files for synteny visualization, the mandatory synteny file for specifying genomic positions of conserved regions and the optional genome annotation file. GSV presents two selected genomes in a single integrated view while still retaining the browsing flexibility necessary for exploring individual genomes. Users can browse and filter for genomic regions of interest, change the color or shape of each annotation track as well as re-order, hide or show the tracks dynamically. Additional features include downloadable images, immediate email notification and tracking of usage history. The entire GSV package is also light-weighted which enables easy local installation. Conclusions: GSV provides a unique option for biologists to analyze genome synteny by uploading their own data set ...

Description: This article discusses multiple domains in MtENOD8 protein. Symbiotic nitrogen fixation occurs in nodules, specialized organs on the roots of legumes. Within nodules, host plant cells are infected with rhizobia that are encapsulated by a plant-derived membrane forming a novel organelle, the symbiosome. In Medicago truncatula, the symbiosome consists of the symbiosome membrane (SymM), a single rhizobium, and the soluble space between them, called the symbiosome space (Syms). The SymS is enriched with plant-derived proteins, including the MtENOD8 protein. Here, the authors present evidence from GFP fusion experiments that the MtENOD8 protein contains at least three symbiosome targeting domains, including its N-terminal signal peptide (SP). When ectopically expressed in non-nodulated root tissue, the MtENOD8 SP delivers GFP to the vacuole. During the course of nodulation, there is a nodule-specific re-direction MtENOD8-SP-GFP from the vacuole to punctate intermediates and subsequently to symbiosomes, with re-direction of MtENOD8-SP-GFP from the vacuole to punctate intermediates preceding intracellular rhizobial infection. Experiments with Medicago mutants having defects in rhizobial infection and symbiosome development demonstrated that the MtNIP/LATD gene is required for re-direction of the MtENOD8-SP-GFP from the vacuoles to punctate intermediates in nodules. The authors' evidence shows that MtENOD8 has evolved redundant targeting sequences for symbiosome ...