[EMBOSS] EMBOSS 6.1.0 release now available
Ryan Golhar
golharam at umdnj.edu
Thu Jul 16 19:09:03 UTC 2009
Any thought on implementing some of the algorithms using CUDA when
possible on GPUs? This could speed up some programs significantly.
ajb at ebi.ac.uk wrote:
> Dear EMBOSS users and developers,
>
> A new version of EMBOSS (6.1.0) is now available for download
> from our ftp server:
>
> ftp://emboss.open-bio.org/pub/EMBOSS/
>
>
> If you use any of the EMBASSY packages (e.g. PHYLIP, VIENNA etc) then,
> as usual, remember to re-download and compile those too.
>
> A new version of the mEMBOSS, the Windows port, is also available from:
>
> ftp://emboss.open-bio.org/pub/EMBOSS/windows/mEMBOSS-6.1.0-setup.exe
>
> Many new capabilities have been added and bugs fixed throughout.
>
>
>
>
> Release highlights for EMBOSS include:
>
> * Full support for the new SwissProt format. In most cases the entry can
> be read and written exactly
>
> * Full support for EMBL and GenBank entries. In most cases the entry can
> be read and written exactly
>
> * Support for FASTQ short read formats for sequence and quality data
>
> * Full support for protein and nucleotide sequence parsing from PDB entries
>
> * Full support for GFF3 feature format as the new default feature output
>
> * Improved summary information at the end of report output
>
> * Alignment output using multiple sequence formats
>
> * Extended support for distance matrix file formats
>
> * Improved support for regular expression and pattern searching
>
> * Improved support for large sequence alignments
>
> * Support for remote locations in feature table processing, for example
> retrieval in coderet.
>
> * Output directory support extended to allow directories to be created
>
> * Normalisation option for hydrophobicity plots (pepwindow and pepwindowall)
>
> * Processing of methylation sites in restriction mapping
>
> * Embossdata reports results alphabetically sorted
>
> * Command line qualifiers should be unique after 5 characters to allow
> safe abbreviation
>
> * Improved configuration procedures for X11 support
>
> * Support for dasgff report format, making it possible to write
> EMBOSS-based DAS annotation servers
>
>
>
>
> Release highlights for EMBASSY include:
>
> * Support for MEME 4.0
>
> * Phylipnew updated to Phylip 3.68
>
> * Support for the HMMERDB environment variable in Hmmernew.
>
> * Bug fixes for the MSE multiple sequence editor
>
>
>
>
> Release highlights for Jemboss include:
>
> * Refactoring of the source code
>
> * Location of the 'Execution mode' menu moved near to the 'Go' button in
> the application forms. When a user runs a job for the first time in
> 'batch' mode an information message is displayed
>
> * Automatic configuration of the standalone Jemboss GUI on
> UNIX systems after typing "make install" for EMBOSS. This
> standalone GUI can be run using the runJemboss.csh script
> in the EMBOSS 'bin' directory. This assumes that you have
> a reasonably up-to-date version of Java installed (1.6
> preferred)
>
>
>
>
> For future extensions, we have added:
>
> * Parsing of cross-reference information from SwissProt and EMBL/GenBank
> formats
>
> * Code to delete and update database indexes
>
>
>
>
> New EMBOSS wiki
>
> EMBOSS now has a Wiki at http://emboss.open-bio.org/wiki where we will
> maintain the master copies of documentation for the applications and
> libraries, and where we have sections for planning new features and
> applications for the next 3 years of funding. Please contribute any
> corrections to the documentation and add new ideas to the "Planning"
> section. We will, of course, be making the wiki prettier as it
> matures.
>
>
>
>
> Important note for Developers
>
> New distributions of operating systems have started to use the series
> 2 version of libtool. We therefore now use this in our CVS
> repository. The latest stable version of libtool is 2.2.6a (reported
> by libtool itself as 2.2.6). Developers using systems with older
> (1.5.x) libtool versions will have to install a local copy of
> libtool. This would typically be done by downloading the source code
> from the GNU site:
>
> ftp://ftp.gnu.org/
>
> After installing libtool it will usually be necessary to then
> re-install autoconf (2.63) and automake (1.11) to the same directory
> root (they are often tied to the version of libtool they were provided
> with). They too are available from the GNU ftp server. Make sure that
> your PATH is refreshed between doing the installations of the GNU
> tools in order that the previous versions aren't referenced.
>
> We note that one system (cygwin) currently provides an experimental
> version of libtool (2.2.7). Developers on these systems (and, in general,
> on any system with a higher version of libtool than in our CVS repository)
> should type:
>
> autoreconf -fi
>
> before attempting compilation. We will usually keep up-to-date with libtool
> stable releases within a libtool series.
>
>
>
>
> New BBSRC funding and future work
>
> As previously announced, we have recently been refunded by the BBSRC.
> What we said in that announcement bears repeating here.
> The core aims of the funding proposal were to continue support,
> maintenance and development of EMBOSS, and to provide extensive online
> training materials for users, developers and system administrators using
> text from a series of books to be published by Cambridge University Press.
>
> We are also explicitly targeting areas where we see EMBOSS can be
> expanded:
>
> * Richer data content in EMBOSS outputs leading to major improvements
> in the integration and visualisation of results in browsers.
>
> * Processing many more data fields in EMBOSS inputs (taxonomy,
> genes, GO terms, cross-references, keywords.
>
> * Extending and improving database access: better indexing, query
> language support and combining searches across multiple databases,
> support for non-sequence data resources and new data access methods
>
> * Scaling up the libraries and adding new applications to support the
> data volumes generated by next-generation sequencing runs. We
> anticipate many more users will be working with short read data
> mapped to reference sequences over the next few years.
>
> * We aim to add at least 100 new applications in these 3 years.
> Suggestions for new applications are very welcome.
>
> * Major work on new developments and new library code will start from
> August.
>
>
> Alan
>
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>
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