EMBOSS: Project Meeting (Jul 12th 1999)

Attendees

Sanger Centre: Peter Rice, Richard Bruskiewich
HGMP: Alan Bleasby, Gary Williams, Jon Ison, Sinead O'Leary, Thon de Boer, Val Curwen
EBI:
EMBnet Italy: Donata Colangelo

1. Matters Arising

None.

2. General progress on release 0.0.4

Alan has implementer profile versions of Smith Waterman (water) and Needleman Wunsch (needle). For database scanning, these run without gaps. Versions with gaps could be the same or separate programs. A range of profiles can be produced.

Alan has added floating point versions of the comparison matrix code.

After discussion, it was agreed that lower case output file names would be preferred by most users. Where users (maybe at Sanger) prefer the name to match the original sequence name this could be put on the command line by scripts.

3. Sequence Features

Peter is still working on this. GFF format input and output with sequences is implemented and will be checked in today. Output of feature tables without sequences needs more work. A simple implementatio of SwissProt and EMBL feature table format is also planned as this affects sequence input and output.

4. Any Other Business

Peter will contribute an article on EMBOSS to the next issue of the Biochemical Society magazine in their Cyberbiochemist section.

5. Next meeting

Monday 19th July, usual time and place. Topics for the agenda include tasks for the first release and a wish list of enhancements to the current programs.

Peter Rice, Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton Hall, Cambridge, CB10 1SA, UK.