EMBOSS: Project Meeting (Jul 6th 1999)
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.
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.