EMBOSS: Project Meeting (Fri 3rd September 2004)


RFCGR/HGMP: Alan Bleasby, Jon Ison, Gary Williams,
Sanger: Tim Carver
EBI: Peter Rice,


1. Minutes of the last meeting

Minutes of the meeting of 20th August 2004 are here

2. Software Development

2.1 Domainatrix

Jon has worked through Ranjeeva's applications. They can now read "any" alignment or sequence format, adapted as simple extensions of FASTA etc.

Documentation has been updated. New functionality that is not needed or over-engineered has been stripped, making it easier to document and use the programs.

2.2 Diffseq

Gary has modified diffseq, as requested by Tim, to show SNPs that change translations. A feature routine has been contributed. There are a few problems to be resolved with frames across multi-exon genes. A microbial version will be passed to Tim for testing at Sanger.

2.3 Jemboss

Alan has Jemboss running on AMD64 with at least one version of Java.

2.4 Phylipnew

Peter has fixed a problem in the old phylip with null characters appearing in species names. No users had reported this - it was found by QA testing.

2.5 XML output

Peter reported that EBI external services have an XML format for tool output which he will consider for EMBOSS output (as outdata and as sequence, feature, report or align output).

2.6 Split entries

Tim requested a program (possibly entrezsplit) to return split entries. This would need to split the feature table without losing feature information - tricky as it involves splitting the sequence, extracting a subset of the feature table, and copying all other text, and also is quite specific to EMBL format.

Output file naming would also be complicated, but can follow the -ossingle model for sequences.

3. Administration

3.1 ACD talk

Peter's postponed ACD update talk will be next Friday (10th).

4.2 User survey

Over 800 replies so far.

4. Documentation & Training

4.1 Books

Alan will revise the book chapter outlines..

5. User queries and answers

Gary's current list reviewed. Most new issues were already answered.

6. AOB

7. Date Of Next Meeting

Next meeting at 9.30 on September 17th, 2004,