EMBOSS: Project Meeting (Jun 7th 1999)


Sanger Centre: Peter Rice, Ian Longden, Richard Bruskiewich
HGMP: Alan Bleasby, Gary Williams, Val Curwen, Thon de Boer, Mark Faller, Sinead O'Leary
EBI: Rodrigo Lopez
Apologies: Martin Senger

1. Matters Arising

2. General progress on release 0.0.4

Peter has updated ACD processing. A new qualifier "-stdout" will prompt the user but will, by default, write output to stdout. There will still be a prompt for the output file in case the users wants to save to a file. There is an EMBOSS_STDOUT variable that can control default settings for this.

SRS 6.0 with application support is now installed at Sanger. Application definitions will be tested in the near future.

Gary commented that Selenocysteine can be represented as "U" in protein sequences. Peter will implement this but with options to exclude it for applications that only support the 'standard' amino acid codes. There are also issues of comparison matrices with no U defined.

John is working on dynamic proramming methods and will be trying new matrices as local data files.

3. Library documentation

Peter has a first draft of the library documentation which will be copied to John and Richard for comments.

4. Sequence Features

Richard described the current status of the "ajfeat" module with an abstract internal representation for DNA and protein sequence features.

First implementation of these is due soon, and will be an extension to seqret to handle input and output of sequence features in any available format.

6. Next meeting

Monday 14th June, usual time and place.
Peter Rice, Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton Hall, Cambridge, CB10 1SA, UK.