Tony writes: {{ double-space-with-newline }} I have just checked in to the Bio::Das perl beta CVS repository (“Bio-Das2”) a collection of modules that creates a minimal DAS reference server from a single AGP file (or a directory of one or more files). There is also a sample server script in the “eg” directory.

Briefly, the server is started using something like:

cd ./eg
./agpserver --dsn ncbi31 --port 3000 --agpfile ./AGP/chr1.agp

It can then be used by a DAS client in the normal way. It is simple (no frills!) and capable of serving assembly information, entry_points, DSN info, features across a segment and features by ID. No other DAS commands are supported yet.

Jason writes:

I’ve added a parser for the ab initio gene predictor GlimmerM in Bio::Tools::Glimmer. Tests are added to t/Genpred.t now.

It follows the Bio::Tools::AnalysisParser interface which support the next_prediction call and returns a Bio::Tools::Prediction::Gene object in the same way as Genscan.

I also have some scripts for building the training set file so you can run Glimmer on other species. There is also a similar script for building custom splice sites file for Genewise which I’ll commit soon. Basically it takes as input a GFF file which has exons annotated (typically from Sim4/Exonerate alignments of cDNA to DNA) and a reference to the genomic DNA db (typically just a flatfile which we index with Bio::DB::Flat).

Hilmar writes:

I got the Oracle version of the biosql schema fully migrated, at least as far as I can tell from here. I’m going to commit the new version some time today. There will also be a sql*plus migration script from pre-Singapore to the current version that supposedly keeps your data intact (be sure to read the disclaimer though).

This means we’re getting ready to release Biosql 1.0, possibly as early as next week. If anyone sees any problems with the current schema that he/she thinks should be corrected before this release, please speak up now. I guess I should make an effort and generate an updated ERD before release; the dated ones are confusing wrt the current schema. If there is consensus I’ll put out a release candidate early next week.

Heikki writes:

Philip Lijnzaad has written a new sequence format module called ’tab’. It is in CVS. Here is the blurb he wrote:

It is very useful when doing large scale stuff using the Unix command line utilities (grep, sort, awk, sed, split, you name it). Imagine that you have a format converter ‘seqconvert’ along the following lines:

my $in  = Bio::SeqIO->newFh(-fh => *STDIN , '-format' => $from);
my $out = Bio::SeqIO->newFh(-fh=> *STDOUT, '-format' => $to);
print $out $_ while <$in>;

then you can very easily filter sequence files for duplicates as:

Nigam Shah has created the necessary PPM/PPD distribution files for bioperl-1.2 .1 that will allow ActiveState perl users on Windows machines to easily install the bioperl suite and the most common bioperl external module dependencies. The PPD file is online at http://bioperl.org/ftp/DIST/Bioperl-1.2.1.ppd. The actual PPD file is at http://bioperl.org/DIST/bioperl-1.2.1-ppm.tar.gz

More information on bioperl Windows installations can be read online at http://www.bioperl.org/Core/Latest/INSTALL.WIN

March 15-16, 2003 – About a dozen Moby developers gathered recently. Minutes from the meeting are online at http://www.biomoby.org/twiki/bin/view/TWiki/CarnegieTAIR and pictures are online at http://biomoby.org/MOBY-DIC-III/MOBYDICIII.html

We need you!

Please download and help test a potential 1.2.1 release candidate that is available at http://bioperl.org/ftp/birney/bioperl-1.2.1-rc2.tar.gz

If all goes well the official bioperl-1.2.1 will be released early next week.

GO::TermFinder will take a list of genes (any name that appears in an annotation file will do, though there are caveats for ambiguous names), an ontology file, and an annotation file, and determine the P_values for the observed frequency of annotation to those genes for each GO node. There are currently some differences between how the P-values are

The full announcement can be read here: http://bio.perl.org/pipermail/bioperl-l/2003-March/011707.html