EMBOSS: Project Meeting (Fri 14th January 2005)
1. Minutes of the last meeting
Minutes of the meeting of 12th November 2004 are
2. Software Development
2.1 Database indexing
Alan described the embindex source code which has grown
Keywords will be implemented as a tree of trees. Aim to add in time
for the next release for index and retrieval. Updating and deleting of
keywords will follow.
2.2 Alignment formats
Peter reported on a major review and bugfix of sequence
alignment output formats, started by a bug report on reversed sequence
2.3 diffseq update
Gary has added an option for diffseq to work with a global rather
than a local alignment.
2.4 Antigenic Regions
Lisa reported a request from Phil Cunningham at King's College
London, who had compared antigenic with the GCG program
peptidestructure on selected SwissProt entries and found the GCG
output may be more accurate (though not perfect) but is very hard to
An EMBOSS version of the Jamieson-Wolf algorithm would be very
useful. Peter noted that he has had a similar request from Schering.
Jon has updated all applications, and incorporated Waqas's and
Mike's code. ACD files and file formats are all updated. Some revisions
are still needed for the PDB parsing paper, especially for better
ligand detection where PDB file markup is poor.
Next month the domainatrix package may be split into 3 smaller parts.
3.1 Release 2.10.0
Alan will add the indexing code.
Peter will complete testing of alignment formats with reversed
DNA sequences and ranges.
Jemboss should use the embassy directory for documentation of EMBASSY programs.
4. Documentation & Training
Docbook tags are proving too complex. General preference was to use a
Word template instead. The deadline for the books is unclear, given
the RFCGR closure.
4.2 Code documentation
Peter is adding category markup for EFUNC, with the aim of
validating categories and ensuring they appear in the correct
"section" of the source file. This will be a gradual process, starting
with string functions.
4.3 Sourceforge website
The cygwin page is incorrect and needs updating. Alan has the details.
5. User queries and answers
Gary's current list reviewed. Most new issues were already answered.
7. Date Of Next Meeting
Next meeting at 9.30 on January 28, 2005,