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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?
JCoa
st 1.
1
JCoa
st 1.
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JCoa
st 1.
3
2008 2009 2010 2011
JCoa
st 1.
4
JCoa
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JCoa
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Public
ation
www.jcoa
st.ne
t
Web
Ser
vice
MPI-Bremen MPI-Bremen & Ribocon GmbH
JCoa
st 1.
6 be
ta
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