EMBOSS: Project Meeting (Jul 6th 1999)


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

1. Matters Arising


2. General progress on release 0.0.4

Alan has replies from Toby Gibson on profil emethods and is implementing Gribskov (profilesearch) and Henokoff (blocks) matrices.

Emma may need updating now that clustalW 1.8 is released.

Ian is working on supermatcher, a Smith-Waterman local alignment application for long sequences with some good quality matches. This is to test algorithms to replace the EGCG quickmatch program which is the last of the EGCG application areas to need urgent attention at the Sanger Centre.

Alan asked for ~/ naming to be implemented for file names. Peter will add this.

There was discussion about legal gap characters. "." "-" "*" and "~" are all known to be used by some sequence formats and applications. It was agreed that EMBOSS would standardise on dots "." and would convert sequences on input.

Martin Senger has informed Peter that someone at the German EMBnet node has successfully implemented ACD files as an interface description for W2H. This would be the first use of ACD to define a web interface.

Donata Colangelo is visiting the Sanger Centre for 2 weeks to work on integrating applications from the Italian EMBnet node into EMBOSS.

3. Sequence Features

Peter is still working on feature input and output.

The issues of input and output file naming were raised. It was proposed that the sequence name should be used as the default for the feature file name (e.g. seqname.gff) on input, with the sequence name in the original case. On output the same would apply. Peter will test these methods and report back.

4. Next meeting

Monday 12th July, usual time and place.
Peter Rice, Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton Hall, Cambridge, CB10 1SA, UK.