EMBOSS: Project Meeting (Apr 10th 2000)
Peter has replaced "seqret" with "seqretall" but added a new "firstonly" option to return a single sequence for sites who depend on only getting one sequence from a run. "seqret" will be added as a "make check" application.
There was discussion about feature coordinates. Should the start and end positions refer to the original sequence or to a selected subsequence? No firm conclusion was reached, especially for output feature tables.
Peter will propose a new validation procedure for sequence ranges with a link to a sequence object and a default range of "all" to replace the present method which is causing complications when -sbegin and -send are specified together with a range.
Peter will propose new attributes and qualifiers to control whether output files are created and/or old files deleted.
Gary would like an application to align two very similar long sequences (about 50kb each). supermatcher is not enough, as it has a limited number of gaps allowed. Gary is looking at sim3 and suffix tree solutions. The output should be a feature table of differences between the two sequences.
Meeting on Monday 17th April, 11:00am, usual place.