[EMBOSS] EMBOSS 4.0.0 released

ajb at ebi.ac.uk ajb at ebi.ac.uk
Sat Jul 15 05:33:48 EDT 2006

EMBOSS-4.0.0.tar.gz is now available. It can be downloaded from the


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.

 - new prompt style generated from 'knowntypes'
 - new -help format provides more information

 - new sequence access method 'dbfetch' uses the EBI's REST services
 - new sequence access method 'mrs' uses CMBI's "Maarten's Retrieval

 - new program backtranambig
 - new program makenucseq
 - new program makeprotseq

 - 'embl' format will read both the old EMBL format and the new one.
     A new output format 'emblnew' can be used to write the new format.
 - new 'swissnew' database format

 - lists of prosite patterns can now be used by fuzznuc, fuzzpro & fuzztran.
     Pattern lists can be specified using the @filename syntax. New
     options added specifically for pattern lists. Pattern lists have a
     new ACD definition type.
 - lists of regular expressions can now be used by dreg & preg

 - Use of GFF for proteins now allowed

 - prophet now uses an 'align' output type
 - iep allows the specification of the number of uncharged lysines
     and intra-chain disulphide bridges
 - splitter/union allow nucleotide deatues to be preserved
 - digest has a ragging capability
 - coderet writes any permutation of cds, mrna & protein to
     separate files
 - mincount option added to wordcount
 - biosed modified to allow the specification of sequence mutation
  - wossname can now search for phrases

 - new sequence type 'gapstopprotein'
 - sequence reading from website URLs now defaults to HTTP 1.1

 - new 'keywords' attribute in ACD files

 - many minor additions, bugfixes and placeholders for future capabilities

EMBASSY packages

VIENNA has been added. This is a port of the Vienna RNA package by
Ivo Hofacker. It is to be regarded as an alpha test. We are
investigating the incorporation of the Vienna sequence format into
the main libraries. This would lead to simplification of the interface
for future releases.

HMMER: this package is now a wrapper written around HMMER 2.3.2
       You must therefore install HMMER 2.3.2 from the
       http://hmmer.wustl.edu/ site and add it to your PATH.

MEMENEW: this package is now a wrapper.
       You must therefore install MEME/MAST from the
       http://meme.sdsc.edu/meme/meme-download.html  site and add it
       to your PATH.

MYEMBOSS: This package enable developers to write their own applications
       using the standard EMBOSS distribution.

PHYLIPNEW: This is now out of EMBOSS beta testing. It is PHYLIP
       version 3.6b

Microsoft Windows

An alpha test version of EMBOSS for Microsoft Windows is available
from the 'windows' directory of the ftp server above. This port was
done using Andre Blavier's EMBOSSWIN package as a starting point and
we thank him for his work.

The EMBOSS programs can be run from a DOS Command window. There is currently
no GUI though we hope that some may spring up from the community.

If, when trying to run applications, you get "DLL missing" errors then
you will need to install the vcredist_x86.exe package for Visual C++
2005 from the Microsoft web site. This small executable does not install
a compiler, only the required runtime DLLs.


Developers should note that we are in the process of standardising
library function names. Old function names will still work but
will print out a 'deprecated' message when compiled using the GCC
compiler. We therefore recommend use of this compiler for developers
as an aid to updating their source code.

Happy St Swithun's (Swithin's) Day.



15th July 2006

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