EMBOSS News

EMBOSS Release 5.0.0

15th July 2007

EMBOSS-5.0.0.tar.gz is now available. It can be downloaded from the directory: ftp://emboss.open-bio.org/pub/EMBOSS/ or via anonymous ftp to emboss.open-bio.org in the pub/EMBOSS directory.

As usual, more complete information is in the ChangeLog file. Here are some highlights:

EMBOSS Release 4.1.0

7th March 2007

EMBOSS-4.1.0.tar.gz is now available. It can be downloaded from the directory: ftp://emboss.open-bio.org/pub/EMBOSS/ or via anonymous ftp to emboss.open-bio.org in the pub/EMBOSS directory.

As usual, more complete information is in the ChangeLog file. Here are some highlights:

• Two new applications edialign and wordfinder
• Full set of 4.0.0 patches included.
• Bugfixes to backtranseq, showseq, NCBI PIR and SwissProt sequence formats, word-matching algorithms.
• Improved support for SRS data access (retrieval by GI number) and fixes to MRS retrieval by accession and ID.
• New sequence format "refseq"
• Improved performance for reading and translating large sequences
• Improved support for the pattern files introduced in 4.0.0
• Extended memory leak testing and extended compiler warnings for developers

EMBOSS Release 4.0.0

15th July 2006

EMBOSS-4.0.0.tar.gz is now available. It can be downloaded from the directory: ftp://emboss.open-bio.org/pub/EMBOSS/ or via anonymous ftp to emboss.open-bio.org in the pub/EMBOSS directory.

As usual, more complete information is in the ChangeLog file. Here are some highlights:

• Support for the new EMBL database format
• Two new sequence database access methods (WsDbFetch from EBI, MRS from CMBI)
• Improved support for reading data over HTTP
• Enhanced help output
• New applications from the EMBOSS team and contributions by users
• New options (requested by users) for many progams.
• Controlled vocabulary of known types for files, strings and other data.

We have also updated the EMBASSY packages

• Vienna RNA package added as a beta release. This fills a long-standing gap in EMBOSS functionality.
• PHYLIPNEW (Phylip 3.6) is now a full release. The version with EMBOSS 3.0.0 was a beta release. We hope for feedback from users and would like to expand our coverage opf phylogenetics applications and data formats.
• HMMER 2.3.2 and MEME wrapped - we found it difficult to keep the early complete code ports up to date so we have changed our approach and wrapped HMMER and MEME as simple wrappers around the command line versions.
• TOPO updated following a user request. Although the author Susan Jean Johns has a new version of TOPO which avoids many of the limitations of version 1, it is no longer in C and harder for us to integrate. By cleaning up the code we have a version of TOPO 1 that no longer has limits on the number of transmembrnae regions in the displayed topology - and has a few other bigs fixed at the same time.
• New MYEMBOSS package for developing users own applications. The MYEMBOSS directory contains everything needed to set up a development environment for EMBOSS without the need to install the complete code base from CVS. This release of emboss includes a frozen view of the library source code on the website and the code databases at EBI. An added benefit is that you will work with code that changes only with each release, not every day. We have used MYEMBOSS in recent programmer training courses, and are looking to expand EMBOSS training.

Announcement of Funding for EMBOSS Core Development and Support

25th April 2006

The UK Biotechnology and Biological Sciences Research Council is funding EMBOSS for 3 years from 1st May 2006.

For more details see the EBI Press Release

EMBOSS Team United at European Bioinformatics Institute

1st August 2005:

Following the closure of their former home institute The Rosalind Franklin Centre for Genomics Research (RFCGR), the remaining EMBOSS development and support team (Alan Bleasby and Jon Ison) have moved to join Peter Rice at the European Bioinformatics Institute, also on the Wellcome Trust Genome Campus in Hinxton near Cambridge, UK.

The EMBOSS team are continuing to look for long term funding and hope to be able to make a further announcement in the near future.

EMBOSS Release 3.0.0

15th July 2005

EMBOSS-3.0.0.tar.gz is now available. It can be downloaded from the directory: ftp://emboss.open-bio.org/pub/EMBOSS/ or via anonymous ftp to emboss.open-bio.org in the pub/EMBOSS directory.