JCoast - A software window into your microbial genomes and metagenomes

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

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? et ta .n e be ic st oa on 2 rv oa Pu 1.1 6 6 3 oa .4 5 1. JC ati 1. 1. 1. 1. Se 1 jc st ic st st st st st st w. eb bl oa oa oa oa oa w W w JC JC JC JC JC JC 2008 2009 2010 2011MPI-Bremen MPI-Bremen & Ribocon GmbHJCoast 1.6 beta 4● 503 Java Classes● 128.155 Physical Lines of Code

JCoast Evolution Version 1.6Version 1.1

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

MicHanThi Annotation Fully automated annotation, based on: BLAST, InterPro, SignalP and TMHMM Assignment of GO-/EC-numbers and Gene names Quality assessmentHuman 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

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)genomes Basic charts already included

Compare (meta)genomesGenome 1 Genome 2

KEGG Distribution ReliabilityJCoast KEGG

Visualize Data Visualize genomes through custom circular plotsExample 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) andNucleotide sequence data (.fsa)●Can be imported into Sequin (NCBIsubmitting and updating tool)●Sequin generates EMBL,GenBank andASN.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 dataClose 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 Report bugs StartJCoast

http://www.jcoast.net Report More bugs Insights StartJCoast

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

Thanks for your attentionVisit us: http://www.jcoast.netPublication:

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JCoast - A software window into your microbial genomes and metagenomes

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