EMBOSS: Project Meeting (Thu 26th Apr 2001)

Attendees

1. Matters Arising

EMBOSS 1.12.0 contains the following new programs in addition to the usual load of library mods/fixes/etc.
Distmat - Creates a distance matrix from multiple alignments of nucleotide or protein sequences. The sequences need to be aligned before running this program. The quality of the alignment is of paramount importance in obtaining meaningful information from this analysis.
Charge - Simple sliding window plot of charge vs position in a protein sequence.
Cai - Codon adaptive index calculation. A measurement of the level of usage of the 64 codons in a sequence.

Alan has checked for memory leakage throughout EMBOSS and has fixed several leaks.

Tim is working on einverted.

Gary has continued with documentation. He is working on prophet, and is looking into incorporating estscan, a HMM for finding open reading frames.

Peter has been working on features. He has removed dictionaries and unwanted definitions. He has code that can read and write feature tables containing all known features in both embl and gff formats. There is a new gff sequence format so that sequences can be stored with features. Where possible, he has modified the applications so that they use feature tables and write report files. Following David Martin's suggestion, he might implement a standard header for report output, which gives the parameters used for running the program. EFUNC functionality has been improved. He will continue with a cleanup of macro names.

2. Date Of Next Meeting

Next meeting to be held on Thursday 10th May, HGMP