EMBOSS: Project Meeting (Jul 19th 1999)


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

1. Matters Arising


2. General progress on release 0.0.4

Alan has implemented "water" and "needle" for local and global gapped alignments.

Alan's profile program uses the same algorithms. It is renamed "prophet" to avoid a name clash. Profiles can be an ungapped frequency matrix or Henikoff and Gribskov formats with gap penalties.

Profiles are built by the updates "prophecy " program.

Peter noted "splitseq" needs to be renamed to avoid a clash with a Staden utility. He will check for other clashes with application names in the default path. The paths at HGMP will also need testing.

For the beta release, the main need is for updated documentation, on applications and command line options. Peter will try to automate this using -help.

Thon will send the latest version of the ACD documentation later this week. Peter will write database documentation in the same style.

Donata's "complex" application needs some modification for filenames and ACD prompts. The "powf" and "modf" calls have been replaced by #defines.

The problem with "stretcher" and an "ALIGN" macro name have been fixed by renaming ALIGN in the source code. This was a problem only on a MachTen Mac Unix system.

The scripts directory is empty. Peter will contribute some of the documentation scripts.

The "embplot" directory is no longer needed.

SSH is now working between HGMP and Sanger.

Alan needs sequence reading to provide a "reread" capability so that sequences can be reloaded after a database search for alignments. Peter will implement this as an extension to ajseq.c for each access method.

The clustalw front end "emma" has been tested with clustalw 1.8 and works.

Alan has added sequence output to "fuzznuc" and "fuzzpro"

3. Sequence Features

Peter will commit the first implementation of "seqretfeat" after the meeting.

Richard will look into adding feature dumping to applications, especially etandem and equicktandem. Peter warned that these have some problems with sequence numbering inherited from the original versions.

4. Any Other Business

5. Next meeting

Monday 26th July, 11:00am, usual place. Topics for the agenda include tasks for the first release and a wish list of enhancements to the current programs.
Peter Rice, Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton Hall, Cambridge, CB10 1SA, UK.