EMBOSS: Project Meeting (Apr 26th 1999)
Guy Slater at HGMP has some EST clustering and frame finding code. Peter will check with him on whether this can be included in EMBOSS.
Thon is working on updates to the ACD documentation, and will also work on documenting the emboss defaults settings and database definitions.
Richard has the CVS tree set up, and plans to work on the GFF code in June/July.
Alan is updating sequence positions in sigcleave (etc.). He has implemented and integrated a number of string pattern matching algorithms. Some code for ranges and mismatches is still needed. Patterns are preprocessed.
Val is working on sequence pretty output formats and looking into restriction enzyme patterns.
Mark if working on clustalw and pepinfo.
Ian has almost finished prettyplot. There are some minor problems with the PLplot graphics library in portrait mode.
Gary has translate using the NCBI tables except for table zero, and is working on utilities to list available databases and programs. Gary will also work on the user documentation.
Sinead is working on motif searching and primer programs.
Database formats were discussed. HGMP would like to index database subsets that they use with FASTA and BLAST. Peter suggested indexing the blast2 index files (he has the format from NCBI). There may be other ways to index whole files and keep using the Staden/EMBL-CD indices.
Database supersets are also needed. Peter will think about this.
Gary suggested looking into the EMBL "CON" division for whole genomes.