Dear users of wrappers4EMBOSS,
This message only concerns you if you are using wrappers4EMBOSS with one of the
following : EMBOSS version 6, a local installation of MRS version 3, fastA,
ps_scan.pl for searching PROSITE, InterProScan version 4.4, a Web Service access
to WU-BLAST and fastA at the EBI.
You might have to upgrade for the following reasons :
- The MYEMBOSS-6.0.0 package does not contain test programs. As a consequence
the installation script of wrappers4EMBOSS failed on a "fresh" installation and
had to be re-run. This bug has been fixed.
- The script mrsget.pl (used to query a local MRS 3 installation) sometimes gave
erroneous results. This bug has been fixed (with help of MRS developer Maarten
Hekkelman).
- The programs fastasearch and fastapid from the fastA module have been modified
so that the entire description line is now included in the output (truncated
description lines can be terribly uninformative...). Bug fixes in both the
"wrapper" and in the fastA suite itself (by "Bill" Pearson after submission of a
bug report) make that it is (again) possible to switch off statistics and obtain
just a list of n best "hits" (in case you might need that). We have also made
the installation of the old fastA version 2 suite for the purpose of pairwise
comparison optional.
- A novelty is that PROSITE pattern matches can be validated using a second
search against a mini-profile. The "wrapper" for ps_scan has been adapted to run
with the latest version of ps_scan.pl and the evaluator.dat file that is
distributed with PROSITE. This validation is performed by default but can be
switched off. This new way of handling PROSITE has also been introduced in
InterProScan version 4.4 and the "wrapper" has been modified accordingly.
- The lists of available databases in the ebi_blast and ebi_fasta programs has
been updated. We can mention that the HGVBASE at the EBI is now at last
searchable by WU-BLAST.
Regards,
Guy Bottu,
Belgian EMBnet Node - wEMBOSS development team
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