EMBOSS: Project Meeting (Mon 4th August 08)
1. Minutes of the last meeting
Minutes of the meeting of 7th July 2008 are
2. Software Development
Jon has identified some applications from Mike's PhD project
that can be added to EMBASSY.
The PCRE regular expression library ha sbeen through several releases
since it was included in EMBOSS. Peter will update the PCRE
library from 4.3 to 7.7. This may allow reporting of all matched to
patterns with a range of lengths which current find one match for each
possible start position.
Nothing to report.
3.1 Release 6.0.0
Release 6.0.0 was produced on schedule (15th July 2008).
Release 6.0.1 was released the same day to fix issues with graphics
and the JEMBOSS interface to mEMBOSS.
4. Documentation and Training
Jon has finished XML validation and checking links.
Jon will write a first draft for an EMBOSS paper covering the
Other papers were also discussed.
5. User queries and answers
There is an outstanding question on fuzznuc results showing
only a subset of overlapping wildcard pattern matches. This is caused
by the PCRE regular expression library - Perl-compatible expressions
find one match for such patterns. See the PCRE library update above.
Phylip sequence format restricts input files to 10 character
identifiers. Longer identifiers cause a failure to read the data but
no message identifying the problem. This can be fixed by testing for a
valid file with longer identifiers, and by testing phylip output for
long or non-unique identifiers.
A user reports that allversusall uses a local alignment and can
report very short local matches.
Peter has been at BOSC and ISMB in Toronto where there was much
interest in EMBOSS. He will report in detail at the next meeting.
7. Date Of Next Meeting
The next meeting is on Monday 18th August.