EMBOSS: Project Meeting (Tue 25th Jan 2000)


HGMP: Alan Bleasby, Gary Williams, Waqas Awan, Jon Ison, Tim Carver, Lisa Mullan
Lion: Peter Rice

1. Matters Arising

Alan reported that EMBOSS 1.9.0 is available. Installation amendment: some sites were experiencing difficulties with autoconf. This was usually manifested by problems installing the ACD files. The installation files have been adjusted to solve this.
Major features of v.1.9.0 are in (1) list file reading: programs will now just give a warning for bad '@'file entries and carry on reading the list. This previously caused program termination and (2) programming libraries: linked lists are now doubly linked. List iteration and string iteration functions have been rewritten.

Jon has been docmenting the scope, nrscope, stamps and domainer applications and associated library code for protein structure. He will commit some of it soon (honest :).

Gary has released the character-based menu 'emnu', and has been ironing out bugs. He is continuing to document programs. He has changed the ajSeqMakeUsa function which sets the USA for a sequence.

Peter has been working on feature reading for EMBOSS. The internal data representation for features is done. All embl-type features can be read in and he will check gff file reading and swissprot reading.

Tim reported on two applications that have been committed. (1) recode: This application scans a given nucleotide sequence for restriction sites. It reports single base positions in the restriction pattern which when mutated remove the restriction site whilst maintaining the same translation. Several restriction enzymes can be specified or alternatively all the enzymes in the REBASE database can be investigated. To find out whether the single point mutations found by 'recode', introduce new restriction sites, 'silent' should be run on the original sequence. ('Silent' searches for silent point mutation sites which maintain the same translation, see 'silent' documentation). The output for 'recode' is similar to the format used by 'silent'. (2) abiview: This program graphically displays the results in an ABI file. The data for each nucleotide is plotted and the assigned nucleotide (G, A, T, C or N) in the ABI file is overlayed on the graphs.

2. Date Of Next Meeting

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