transposable elements (TES) is composed of a major fraction of the many genomes of plants and known to promote the organization and their evolution. Some studies suggest that those elements that repeatedly has an important role in shaping the noncoding regions of the genome such as microRNA (miRNA) locus, which is a component of the mechanism of post-transcriptional regulation.
Although several studies have reported the initial formation of miRNA loci of TE sequences, especially on the plant model, the approach does not use a system that will allow the results to be delivered by the user-friendly database. In this study, we identified 152 miRNAs precursors overlap TES in 10 species of plants. Plante-MIR DB is designed to assemble this data and send it to the scientific community interested in miRNA origin, evolution, and regulatory pathways. Users can search the database through a web interface and search for entries using a variety of parameters. This resource-cross with repetitive elements (Repbase Update) and miRNA (miRBase) repository, where the sequence can be examined for further analysis.
VRprofile: gene-cluster-based detection of virulence properties and the profile of antibiotic resistance encoded in the genome sequence of the pathogenic bacteria.
VRprofile is a Web server that facilitates rapid investigation of virulence and antibiotic resistance genes and genetic context of the widespread nature of this related displacement, the new genome sequencing of pathogenic bacteria. The used database backend MobilomeDB first built in set of known gene loci cluster types of bacteria III / IV / VI / VII secretion system and genetic elements of mobile, including elements of integrative and conjugative, prophages, class I integrons, IS elements and pathogenicity / antibiotics island of resistance .
Thus VRprofile can co-localize these homologs conserved gene clusters using HMMer or BLASTp search. With the integration of the search module cluster of genes homologous to the sequence composition module, VRprofile has shown better performance for the island-like regions predictions than other methods widely used. In addition, VRprofile also provides an integrated Web interface to align and visualize groups of genes identified by gene clusters MobilomeDB-archive, or different sets of bacterial genomes. VRprofile may contribute to meet the increasing demands re-annotation of bacterial variable regions, and assistance in real-time definition of a group of disease-relevant genes in pathogenic bacteria of interest.
DIDA: Distributed Indexing Dispatched Alignment.
One of the important applications in bioinformatics influenced by high-throughput sequencing data sequence alignment flooding is a problem, in which a nucleotide or amino acid sequences are asked about the target to find an area close similarity. When the request is too much and / or the target is too large, the alignment process becomes challenging computing. This is usually handled by preprocessing techniques, where the demand and / or targets that are indexed for easy access when searching for a match. When the target is static, as in the reference genome is established, indexing costs are amortized using the index generated.Product not found
However, when the targets are non-static, such as contigs in the intermediate steps of the assembly process de novo, the new index should be calculated for each run. To overcome the scalability issues like that, we now DIDA, novel framework that distributes indexing and alignment tasks into subtasks that smaller cluster of computing nodes. It provides a workflow beyond the common practice embarrassingly parallel implementation. DIDA is a framework is scalable and modular cost-effective to sequence alignment problems in terms of memory usage and runtime. It can be used in large scale alignments to construct genome and intermediate stages of de novo assembly runs.