A library of parallel methods for dot plot. The comparison of genomes using DotPlots is a traditional problem with high memory and CPU time requisites. Those requisites can be reduced redesigning the DotPlot process and using HPC techniques in its development.
We have developed a library for genomic dotplot and handle large sequences.
Many bioinformatics tools are available on-line but due to rapid developments of new and improved tools, it is necessary to be able to publish and maintain metadata about such tools in a public registry. This metadata can be used to provide several necessary functionalities, for example discovery, invocation and documentation of tools, data persistence systems (data provenance).
Tools available over the internet are particularly useful in biomedical informatics, where large computational resources, both hardware and services; and access to large and constantly updating data collections are basic requirements for solving many typical problems. This is the main motivation for delegation of tool invocation (execution) to remote servers with required computational resources. Common approaches to such distributed tools are web-services (software systems designed to support interoperable machine-to-machine interaction over a network) and workflows (pre-defined organized invocations of web-services).
Here we offer the implementation of a repository for knowledge-discovery-related tool metadata. We use existing formats for tool descriptions and we have also defined a core set of metadata for tools. This metadata is connected to the tool description and improves the possibilities of finding the right tool description among a large set of tool descriptions. The repository allows tool requestors to filter available tools depending on the metadata that the tools are annotated with.
The comparison of genomes using DotPlots is a traditional problem with high memory and CPU time requisites. Those requisites can be reduced redesigning the DotPlot process and using HPC techniques in its development. We have developed a library for genomic dotplot and handle large sequences.