Features

JCoast, a Java-based Comparative Analysis and Search Tool for prokaryotic genomes, makes use of the standardised genome processing and storage system, GenDB. JCoast offers individual and cross (meta) genome annotation by handling several projects simultaneously and assists the biologist in exploration of large and complex datasets. The major improvement rises from JCoast's ability to facilitate rapid and comprehensive comparison of a reference genome with respect to additional genomes, and even metagenomes. It was designed to allow biologists a rapid overview of genome and metagenome projects, using sortable tables to display the information. The JCoast workbench provides search tools and statistical methods to efficiently and intuitively answer questions of comparative genomics. With JCoast you can annotate, analyze, compare, group, describe, export and refine your genomic data through an intuitive user interface.

JCoast supports several standard bioinformatic tools and databases for similarity searches and HMM profiling.

Tools:

• BLAST
• HMMER

Databases:

• NCBI-nr
• UniProt/Swiss-Prot
• Kegg Genes
• genomesDB
• COG
• InterPro
• Pfam

JCoast GUI

• Sortable tables with project content overview
• Extensive Pfam model search functionality, including graphical displays of domain structure
• Creation of custom gene-groups
• Merging of projects for cross-genome analysis
• Taxonomic restriction of search functions (e. g. group-specific genes)

JCoast is compatible with the GenDB v2.2 data model. However, it is frequently adjusted to introduce new features, including compatibility with new or custom databases.

The JCoast installation is simple. It either integrates into existing GenDB installations, can be used standalone on any computer with a precomputed MySQL database, or connects via a web service module to dedicated servers. This flexibility and portability allows the handling of genome projects private and disconnected (in-house centralized) or shared between partners all over the world via the www.

In addition to the graphical front-end, JCoast includes a complete Java application programming interface (API) to write custom classes for individual research questions, purposes, and needs.

Genomic Data access:

JCoast supports two ways to access genomic data, direct through a MySQL server or via a remote Web Service on dedicated JCoast servers.

Direct MySQL access

JCoast supports connectivity to MySQL servers with access to GenDB v2.2 compatible GPMSDB and project databases.

Remote Webservice access

 Triggered by the technological requests of the Microbial Interactions in MArine Systems (MIMAS) project, JCoast was extended to fulfill future requirements and facilitate comprehensive analysis of the genomic data generated within the project. The extension includes various new functions related to statistical data analysis and visualization, mapping of genes to metabolic pathways, as well as an Representational State Transfer based web service. REST is a key design idiom that embraces a stateless client-server architecture in which the web services are viewed as resources and can be identified by their URLs.