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Java add-on to GenDB V2.2 for comparative genomics. |
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Welcome to the homepage of the JCoast software tool. Current version: 1.5 What is JCoast? - More info... [November 10th, 2009] Broken SwissProt Reference As you may already notice, the SwissProt reference link is not working anymore. The SwissProt links are now served by the UniProt Consortium. To view the reference through the UniProt website substitute the old link under 'Edit->Preferences->Observation->SwissProt' with this new 'http://www.uniprot.org/uniprot/”. This link will be also default in the next JCoast release. [August 27th, 2009] JCoast Version 1.5 released A new version of JCoast is available including new features and bugfixes: All occurring KO (KEGG Orthology) numbers are now mapped against KEGG pathway functional hierarchies and can be analyzed and compared. All zoom factors can now be stored as .png. Each gene color can now be adjusted to the default JCoast style or do show matching cog categories. To use this feature, first store the results of Statistic Cog Distribution' analysis to the database by choosing the right mouse 'Store results to DB' option. The panel has been reordered and sorted to provide a better overview and functionality. Further, calculations can be individually run for the DNA-type genome or plasmid. The best observation for each tool can be viewed by moving the mouse over the locus column inside the tabular browser for CDS. The feature is off by default and can be adjusted inside the preferences. In order to keep the whole annotation frame visible also by running JCoast with small screen resolutions, the frame size calculation has been overworked. You can run JCoast via Webstart in the download section. [July 13th, 2009] JCoast Version 1.4.1 released A new version of JCoast is available. Including a fix for the InterPro Prosite e-value parsing bug. You can run JCoast via Webstart in the download section. [July 1th, 2009] JCoast Version 1.4 released A new version of JCoast is available. You can run JCoast via Webstart in the download section. [October 27th, 2008] JCoast Version 1.3 released A new version of JCoast is available. Including several bug fixes, many new statistics and a neighbourhood browser for genomesDB observations. You can run JCoast via Webstart in the download section. [April 24th, 2008] JCoast source code repository at Bioinformatics.Org A JCoast group has been created at www.bioinformatics.org. The JCoast source code can be downloaded via the SVN repository browser. [April 3rd, 2008] JCoast paper published Richter, M., T. Lombardot, I. Kostadinov, R. Kottmann, M.B. Duhaime, J. Peplies, and F.O. Glöckner. JCoast - A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes. BMC Bioinformatics 2008; doi:10.1186/1471-2105-9-177 [March 11th, 2008] JCoast now also used for business-related routine applications JCoast is now used within the framework of the genome data analysis service of the company Ribocon, a spin-off of the Max Planck Institute for Marine Microbiology in Bremen, Germany. The Ribocon data analysis service offers advanced ORF prediction and automatic gene annotation for genomic and metagenomic DNA contigs including comprehensive support for users from academia and industry. The Ribocon genome analysis team about JCoast: "This Java-based software represents a perfect solution for our genome analysis service since it allows us to return processed raw data to our customers plus a freely available, platform-independent and at the same time extremely powerful tool for subsequent data visualization, exploration and further analysis. This perfectly matches to our understanding of usability." The JCoast development team and the genomes team at Ribocon are working in close contact and the feedback from the Ribocon customers will help to extend and improve the JCoast software in a highly user-orientated way in the future. [February 25th, 2008] JCoast Version 1.1 released A new version of JCoast is available. Including several bug fixes and a new multi-annotation functionality. You can run JCoast via Webstart in the download section. [January 10th, 2008] JCoast Kubuntu LiveCD Automatic Linux + JCoast V1.0. The current version is available based on the Linux distribution Ubuntu 7.04 and the K Desktop Environment (KDE) 3.5! Read more about in the download section. [January 10th, 2008] JCoast Version 1.0 released Finally it's done. JCoast first stable release. Read more about in the download section. [June 11th, 2007] New logo added The new JCoast logo designed by David Todd, New York, USA (davidevantodd ( at ) gmail.com) is now online. [February 23rd, 2007] Background The sequencing of genomes and metagenomes has today become a standard technique in molecular biology. Nearly unlimited sequencing capacities exist worldwide provided on demand by e.g. the Joint Genome Institute, the Craig Venter Institute or Genoscope. After obtaining the sequences of an organism or community of interest for most investigators, without strong bioinformatics background, a question arises: "What should I do with it now?". The analysis of thousand of genes and the comparison of the content with published information is far from being trivial and requires, besides the "Know-How", a huge amount of computational power. This situation is similar to what we focussed at MPI around 7 years ago when we got our first seven million AGCTs for the Planctomycete Rhodopirellula baltica sequenced. No "turn-key" software systems was available that helped us to answer our biological questions. So, we decided to build up a genome analysis infrastructure and develop software solutions to investigate genome and metagenome data especially from environmentally relevant microorganisms and to compare the data with publicly available information. With this mini-workshop we want to share our accumulated knowledge about gene-prediction, annotation and comparative genomics and pay respect to several requests by researchers that had asked us how they could analyse their recently obtained sequence information from their "hobby-horses". Agenda The workshop will focus on:
Location When: March 13, 2007 Time: 11:00 to approximate 17:00 h Location: Max Planck Institute for Marine Microbiology in Bremen, Seminarroom 4021 and PC-lab How to reach the institute Contact: eu-workshops(at)mpi-bremen.de If you are interested in participating, please send an e-mail to eu-workships(at)mpi-bremen.de until the first of March. Additional information The Microbial Genomics Group (MGG) Last updated: 24.04.2008 |