EMBOSS: Project Meeting (Sep 13th 1999)


Sanger Centre: Peter Rice, Ian Longden, Richard Bruskiewich
HGMP: Gary Williams, Jon Ison, Sinead O'Leary
Apologies: Alan Bleasby

1. Matters Arising

The Linux build problems are resolved.

Richard's 'arbitrary alphabet' applications are intended for comparisons of feature tables.

2. General progress on release 0.0.4

Richard, Peter and Ian will meet later in the week to try a Windows NT build. David Mathog (Caltech) is also interested in NT and VMS versions.

3. Beta Release

EMBOSS was be announced on the embnet.general and bionet.software newsgroups this week.

Gary has aded "merger" to align ends of sequences at HGMP. This is a global alignment with a very high gap opening penalty.

Some users would like multiple pattern searches, for example with fuzznuc.

Multiple runs of pattern matching could make multiple GFF output files. There was discussion on how multiple GFF files could be reused. The result was a specification that multiple GFF files concatenated together could be read and the sequence name checked against the input sequence. This means reading an entire GFF file into memory for opne or more input sequences. This is also useful for GFF files and FASTA files with multiple sequences. GFF reading does not cope well with this yet but can be easily modified.

Peter is working on code to read sequences from blast1 and blast2 indexed databases. This will read directly from the databases but will include generating optional EMBOSS entryname and accession number index files for both formats.

Val is working on generalized sequence formatting and printing. Peter has had other requests for this kind of application.

4. Bruges Workshop

The second EMBnet EMBOSS Workshop is on September 23rd in Bruges. Peter and Alan will be there and will give talks and demos in the morning. The afternoon will be used for discussions on various topics.

5. Any Other Business

6. Next meeting

Next meeting Monday 20th September, 11:00am, usual place.

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