EMBOSS: Project Meeting (Mon 4th January 10)
Mahmut noted that documentation is still needed for needleall before the release. These can be built from the existing needle documentation.
Mahmut has updated wordmatch to search for sequence adaptors, with added statistical information. The changes are being tested by a user. Run times are looking good. The adaptor sequences are compared to a FASTQ file. Half the run time is for processing input, and half for the method.
Peter has committed new sequence formats for genpept refseq and refseqp which were all using the GenBank parser.
Before the release we should check that all updates in 6.1.0 patches are also committed to CVS.
Mahmut has updated jalview in Jemboss.
Jon is considering whether to include Sequence Ontology (SO) terms as synonyms.
Peter will write scripts to check the "to do" comments in the XML sources, and to check application names are marked up.
Jon will clean up the markup and update style sheets to highlight application names.
Peter attend an ENSEMBL workshop on next generation sequencing. There was discussion of quality scores, and the possibility of replacing phred scores with likelihood values for each possible base. We can extend the Accuracy data in a sequence object to handle this, if the core repositories agree to change.