JCoast is a Java-based software for comparative genomics that provides automated annotation, consistent manual annotation, comparison of genomes and metagenomes, custom visualization of data, preparation of sequences for submission to databases, and collaboration features. It is developed by researchers at MPI-Bremen and Ribocon GmbH to provide turn-key genome analysis and data mining without programming. Upcoming updates will integrate more metadata and experimental data types to facilitate multi-omics analyses.

1. A software window into your microbial
genomes and metagenomes
Michael Richter
Molecular Ecology Breakfast Seminar
02.12.2010

2. What is JCoast?
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Java-based COmparative Analysis and Search Tool
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Software for comparative genomics
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Application Programming Interface (API)
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Graphical User Interface (GUI)
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Representational State Transfer (REST) Interface
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Build on top of the established annotation and storage system GenDB
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Open Source software, released under GPL3
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Biologists need biologist-centric software
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Turn-key systems that work out of the box
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Expandable and open for additional modules
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Data-mining without programming efforts

3. Who is developing JCoast?
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2008 2009 2010 2011
MPI-Bremen MPI-Bremen & Ribocon GmbH
JCoast 1.6 beta 4
● 503 Java Classes
● 128.155 Physical Lines of Code

4. JCoast Evolution
Version 1.6
Version 1.1

5. What is JCoast for?
Assist your prokaryotic (meta)genome analysis in:
1) auto-annotation (MicHanThi)
2) consistent annotation
3) comparison of data
4) custom visualization
5) sequence submission
6) cooperations with colleagues

6. MicHanThi Annotation
Fully automated annotation, based on: BLAST, InterPro, SignalP and TMHMM
Assignment of GO-/EC-numbers and Gene names
Quality assessment
Human vs best BLAST Human vs MicHanThi Human vs RAST
20%
30%
50% 50%
70%
80%
Differences Matches Differences Matches Differences Matches
Quast, PhD Thesis 2009

7. Consistent Annotation
In-depth gene function analysis based on KEGG, NCBI-nr, SwissProt,
genomesDB, COG, Pfam, InterPro, SignalP, TMHMM
● Annotate
● Add
● Edit

8. Compare (meta)genomes
Based on distribution of: KEGG, COG, genomesDB, RBMs,
PFAM, SCP, Public databases (hypo, conserved, functional)

9. Compare (meta)genomes
Basic charts already included

10. Compare (meta)genomes
Genome 1 Genome 2

11. KEGG Distribution Reliability
JCoast KEGG

12. Visualize Data
Visualize genomes through custom circular plots
Example shows all [D] Cell cycle control, cell division, chromosome partitioning

13. Visualize Data
Visualize genomes through custom circular plots
Example shows all [D] Cell cycle control, cell division, chromosome partitioning

14. Visualize Data
Visualize genomes through custom circular plots
Example shows all [D] Cell cycle control, cell division, chromosome partitioning

15. Visualize Data
Visualize genome synteny based on genomesDB

16. Prepare Sequences for Submission
●Exports to Feature Table (.tbl) and
Nucleotide sequence data (.fsa)
●Can be imported into Sequin (NCBI
submitting and updating tool)
●Sequin generates EMBL,GenBank and
ASN.1 formats
● Add sequence source modifiers

17. Cooperate with Colleagues
 Representational State Transfer (REST) architecture for XML-based data exchange
 MPI Server: https://projects.mpi-bremen.de/jcoast-rs

18. Integrate third-party data
Close cooperation with Decodon GmbH, Greifswald, www.decodon.com
Integration of 2D gel electrophoresis data via Web Service

19. http://www.jcoast.net

20. http://www.jcoast.net
Start
JCoast

21. http://www.jcoast.net
Report
bugs
Start
JCoast

22. http://www.jcoast.net
Report
More bugs
Insights
Start
JCoast

23. JCoast Outlook
First half of 2011
● Switching genomesDB source to from local to www.megx.net
● Access to comprehensive metadata for all full/draft genomes
and metagenomes
● Implementing an Experiments data-structure to handle
● DNA Array results
● Transcriptomic results
● User-defined experiments
● JCoast workshop at the MPI
● Realized in the frame of the MIMAS project

24. Thanks for your attention
Visit us: http://www.jcoast.net
Publication: