EMBOSS: Project Meeting (Mon 20th August 07)
Currently jaspextract simply checks a JASPAR distribution is correct and copies the files unchanged.
The jaspscan application implements the search methods available through the JASPAR web pages.
Alan has also added a "make check" application dbxstats to report statistics from dbx indices for users in EBI external services.
Peter is expecting a contribution of a Smith-Waterman database search application.
Peter has added PDB files as formats for sequence data. The files have sequence data in two places. The ATOM records are the residues in the structure, and the SEQRES records are the residues in the original sequence. In some cases they may not agree. Sequence format "pdb" reads the ATOM records and is tested for by default. The SEQRES records are read by sequence format "pdbseq" which must be explicitly requested.
Alan and Peter have updated the reading of "CCF" format protein structure files to read both the new and old records so that previous inputs continue to work for the psiphi program.
Mahmut has been looking into XML output options for reports, features and sequences. He has installed BlueJay from source and is looking at compatible XML formats we can use to exchange data.
EMBOSS 5.0.0 services all passed QA testing except for the psiphi problem described above.
Old EMBOSS 2.8.0 services produce different results in a few cases. Peter will investigate. Most are insignificant. A few applications (cusp and emma) have unknown qualifiers and no longer support the exact 2.8.0 commandline.
Alan is investigating a reported problem with launching primer3 on Windows.
Jon, Alan and Peter had a lunch meeting with Cambridge University Press to discuss progress on the three books and to update the main author list.
profit should work only with frequency input. It accepts profiles but is unable to handle gap penalties.
prophet has been run by some users as a profile database search. It would be better to add a new version with a threshold value that only reports "hits" rather than reporting the best match for every input sequence. This will need a new name.
The next meeting is on Monday 3rd September.