EMBOSS: Project Meeting (Nov 1st 1999)
EMBOSS can already read the index files directly from the EMBL database CD-ROM distribution for EMBL and SwissProt.
Documentation on database definitions is needed. Peter will write a comprehensive guide once the new formats are implemented.
Sequence type testing has occasional problems, for example aligning two sequences needs a decision on the type of the first sequence. A length limit will be set of testing DNA or protein sequence type so that any sequence longer than, for example, 50 characters and containing only DNA base codes will be set to nucleotide and not protein. In testing a protein sequence this would result in a warning message only for now. The previous problem of short SwissProt entries should be resolved by using the database type and sequence format where this is informative.
Alan has a new application "plotorf" which plots open reading frame information.
Alan modified the output of MSF format to add missing dots on the checksum line. Peter will check on the general handling of MSF format.
Alan has generated an RPM file for EMBOSS available from the HGMP FTP server.
Implementing a new release number, which should be done soon because of the number of changes, is a simple change to the automake file.
"emma" had some problems caused by waiting for a child process when there were other child processes open (e.g. reading a database with SRS). The code in "emma" now explicitly waits for the "clustalw" process to exit.
"tmap" had a bug when reading single sequences which has been fixed. This was a bug in the original version.
Alan has updated "syco" and "chips".
Ian is working on Will Gilbert's MSE editor. Most of the operations are working. This application will need to prompt the user for additional sequences, but will use the ACD file to startup.
Next meeting Monday 8th November, 11:00am, usual place.