Links

Professional Bioinformatics Support

Ribocon GmbH

http://www.ribocon.com/

Bioinformatics & Molecular Diagnostics

Whatever your task in microbial DNA sequence analysis is - doesn't matter if routine application or cutting-edge project, single sequence read or next generation sequencing data. Ribocon has the infrastructure and the expertise to analyse/integrate your data and to provide valuable support. You can focus on the essential.

Ribocon is our main sponsor and uses JCoast for business-related routine applications.

Databases

Collection of bioinformatic databases.

ARB-Silva

http://www.arb-silva.de/

A comprehensive on-line resource for quality checked and aligned ribosomal RNA sequence data, free for academic use.

SILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya).

SILVA are the official databases of the software package ARB.

megx.net

http://www.megx.net/

Megx.net allows access to integrated environmental and (meta)genomic data intended for use in marine microbial ecology.

By integrating genomic, metagenomic and ribosomal RNA data with primary environmental data and curated metadata, we aim to offer researchers new analytical perspectives in marine ecological genomics.

Projects using JCoast

CONSOLIDER project

http://eigr.grupoei.com/i/i8031/index_i.php

The Project aims at generating at least 100 metagenomic libraries from pristine and contaminated sites throughout the Iberian Peninsula, constituting the first collection with the biological potential of soils and sediments in the Iberian Peninsula. The libraries will be made available to the scientific community. The Project will also explore new ways to preserve the microbial diversity of soils in Spain.

JCoast has been used for teaching purposes and metagenome analysis of the anoxic brackish sediment of a shallow lake originated by human activity.

MIMAS

http://www.mimas-projekt.de/mimas

MIMAS stands for Microbial Interactions in MArine Systems.

The project aims at the establishment of sustainable modern genomic and molecular techniques in the national marine partner institutes in order to support future ecosystem research initiatives.

JCoast will be used facilitate comprehensive analysis of the genomic data generated within the project.

Software

GenDB

http://www.cebitec.uni-bielefeld.de/groups/brf/software/gendb_info/

GenDB is a genome annotation system for prokaryotic genomes. The system has been developed as an extensible and user friendly framework for both bioinformatics researchers and biologists to use in their genome projects. The GenDB annotation engine will automatically identify, classify and annotate genes using a large collection of software tools. Many groups view this automatic annotation as the first step that needs to be followed by expert annotation of the genome.

JSpecies - Taxonomic Thresholds

http://www.imedea.uib-csic.es/jspecies/index.html

JSpecies is an easy to use, biologist-centric software designed to measure the probability if two genomes belonging to the same species or not.

Software, web-based

Metabar

http://www.megx.net/metabar

MetaBar is a spreadsheet and web-based software tool designed to assist users in the consistent acquisition, electronic storage, and submission of contextual data associated to their samples.

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