Dear Colleagues,

We are pleased to announce several new features and data additions to  
dictyBase.

• Orthologs from eight different species (D. purpureum, H. sapiens, M.  
musculus, D. melanogaster, C. elegans, S. cerevisiae, A. thaliana, and  
E. coli) are now available from a new tab on the gene page. The D.  
purpureum ortholog analysis, which conversely is also available from a  
tab on the D. purpureum gene page, has been provided by Adam Kuspa.  
All other ortholog data have been obtained from InParanoid and  
OrthoMCL. The ortholog information is also available for download as a  
tab-delimited file. See examples on the gfm1 (http://dictybase.org/gene/DDB_G0270482/orthologs 
), elmoA (http://dictybase.org/gene/DDB_G0278051/orthologs), or for D.  
purpureum, DPU_G0054104 (http://genomes.dictybase.org/purpureum/gene/DPU_G0054104/orthologs 
) gene page.

• The dictyBase universal BLAST server (http://dictybase.org/tools/ 
blast) contains several new databases:
		• D. fasciculatum CDS and protein
		• P. pallidum CDS and protein
		• Non-coding transcripts, such as RNAs and pseudogenes
		• The 'D. discoideum genomic sequences - DNA' database now includes  
the genomic DNA of non-coding sequences

• The right side bar now contains newly published papers. Every  
Monday, dictyBase imports citations of publications newly indexed in  
PubMed, which are then displayed on the side bar.

• Improved searching behavior: DDB_G IDs, when also serving as gene  
names, can now be retrieved by searching on "Gene Names Only".

• The downloadable sequences and annotations in GFF3 format now  
contain annotated pseudogenes.

• The Stock Center search (http://dictybase.org/db/cgi-bin/dictyBase/SC/searchform.pl 
) for strains now searches for 'All' fields by default, not just names  
and descriptors.

• The confirmation e-mail of shipped Stock Center orders now include  
the reference from the depositor to remind users to cite the original  
work of the depositor when publishing data using the materials  
obtained from the Stock Center.

We hope you enjoy these additions and improvements.

Best regards,

The dictyBase Team
http://dictybase.org