EMBOSS: Project Meeting (Tue 26th Feb 2000)


HGMP: Alan Bleasby, Gary Williams, Waqas Awan, Jon Ison, Tim Carver, Lisa Mullan, Ranjeeva Ranasinghe
Sanger: Val Curwen
Apologies: Peter Rice

1. Matters Arising

Alan has been implemeting 64 bit operation in ajfmt.c. Most C datatypes have changed in the libraries. Notably ints are now "ajint"s and longs are now "ajlong"s. An ajint can be equal in size to an ajlong depending on the hardware; however, an ajlong should be used whenever a 64 bit int might be used. He will work on 64 bit strings next.
ajFmtScanS has been added. This can be regarded as the EMBOSS version of the C function sscanf and operates similarly. It has several extensions, particularly %S is used for dynamically allocated string objects (AjPStr). This function makes reading data files considerably easier. Many applications need to be modified to use it rather than having to rely on tokenisation.
The application hmoments for calculating hydrophobic moments has been added.
The application complex has been delegated to the 'make check' area.
There will in the future be a new EMBOSS release on each bug fix and we will maintain a change log for the different versions.

Jon has written acd files and documentation for several new applications that might appear in EMBOSS this year:
blasts - runs BLASTP on SCOP family members (can be made into a generic blast wrapper)
groups - groups sequence on basis of sequence similarity
pairsub - calculates residue pair substitution matrix
scopseq - read embl-like format scop file and writes a file of sequences
weights - produces weights for a sequence set
siggen - generates a sparse protein signature
sigscan - signature III pattern matching algorithm
sigplot - generates gnuplot data files of signature performance
libgen - generates a library of sparse protein signatures
libscan - scans a library of sparse protein signatures
He is working on the contacts (calculates residue contacts from clean coordinate files) and stamps (runs STAMP over SCOP families) applications.

Gary has submitted the marscan application that finds a bipartite sequence element that is unique for a large group of eukaryotic MARs/SARs (matrix/scaffold attachment regions). He has done some documentation.

Tim has been patched abiview. He is working on the dist program for calculating evolutionary distances between pairs of aligned sequences.

Lisa has reported several bugs and suggestions while working through EMBOSS.

2. Date Of Next Meeting

Next meeting to be held on Monday 5th March, HGMP