[EMBOSS] EMBOSS 6.1.0 release now available

[Ryan Golhar]

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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