[EMBOSS] EMBOSS 6.1.0 release now available

[ajb at ebi.ac.uk]

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