A software window into your microbial genomes and metagenomes

Michael Richter

Molecular Ecology Breakfast Seminar02.12.2010

What is JCoast?

● Java-based COmparative Analysis and Search Tool

● Software for comparative genomics● Application Programming Interface (API)

● Graphical User Interface (GUI)

● Representational State Transfer (REST) Interface

● Build on top of the established annotation and storage system GenDB

● Open Source software, released under GPL3

● Biologists need biologist-centric software● Turn-key systems that work out of the box● Expandable and open for additional modules● Data-mining without programming efforts

Who is developing JCoast?

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2008 2009 2010 2011

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www.jcoa

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MPI-Bremen MPI-Bremen & Ribocon GmbH

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JCoast 1.6 beta 4

● 503 Java Classes

● 128.155 Physical Lines of Code

JCoast Evolution

Version 1.1

Version 1.6

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

70%

30%

Human vs best BLAST

Differences Matches

20%

80%

Human vs MicHanThi

Differences Matches

MicHanThi AnnotationFully automated annotation, based on: BLAST, InterPro, SignalP and TMHMM

Assignment of GO-/EC-numbers and Gene names

Quality assessment

50% 50%

Human vs RAST

Differences Matches

Quast, PhD Thesis 2009

Consistent Annotation In-depth gene function analysis based on KEGG, NCBI-nr, SwissProt,

genomesDB, COG, Pfam, InterPro, SignalP, TMHMM

● Annotate

● Add

● Edit

Compare (meta)genomesBased on distribution of: KEGG, COG, genomesDB, RBMs,

PFAM, SCP, Public databases (hypo, conserved, functional)

Compare (meta)genomesBasic charts already included

Compare (meta)genomes

Genome 1 Genome 2

KEGG Distribution Reliability

JCoast KEGG

Visualize DataVisualize genomes through custom circular plots

Example shows all [D] Cell cycle control, cell division, chromosome partitioning

Visualize DataVisualize genomes through custom circular plots

Example shows all [D] Cell cycle control, cell division, chromosome partitioning

Visualize DataVisualize genomes through custom circular plots

Example shows all [D] Cell cycle control, cell division, chromosome partitioning

Visualize DataVisualize genome synteny based on genomesDB

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

Cooperate with Colleagues Representational State Transfer (REST) architecture for XML-based data exchange

MPI Server: https://projects.mpi-bremen.de/jcoast-rs

Integrate third-party data

Close cooperation with Decodon GmbH, Greifswald, www.decodon.com

Integration of 2D gel electrophoresis data via Web Service

http://www.jcoast.net

http://www.jcoast.net

StartJCoast

http://www.jcoast.net

StartJCoast

Reportbugs

http://www.jcoast.net

StartJCoast

ReportbugsMore

Insights

JCoast OutlookFirst 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

Thanks for your attention

Visit us: http://www.jcoast.net

Publication: