NEWS

February 1, 2010

3 new annotation updates.

New feature: DNA motif search tool to allow searching for DNA motifs in all strains available in this database. Results can be downloaded in both comma-separated value and tab-delimited format.

New batch download feature: Ability to download high-precision ortholog predictions from links in genome menu pages (e.g. Orthologs under "Download" tab of J2315 menu) as well as the main downloads page.

New analyses in GBrowse. Computationally-predicted Rho-independent terminators (TransTermHP) and palindromes (EMBOSS). Click here to view an example.

Fixed bug in updates log search that was preventing results from being returned.

Reference sections of gene summary pages now contain full literature citations (previously included just the PMID).

January 14, 2010

7 new annotation updates.

Strain names updated. Burkholderia cepacia strain AMMD changed to Burkholderia ambifaria strain AMMD (Coenye et al., 2003). Burkholderia sp. 383 changed to Burkholderia lata strain 383 (Vanlaere et al. 2009). We acknowledge Deborah Yoder-Himes (Harvard) for bringing this to our attention.

New ortholog group classification system for Burkholderia orthologs (example view and listing for group BG005276). For more details on the method, click here.

Integration of new links to IslandViewer view of analyses predicting genomic islands. IslandViewer is a computational tool that integrates two sequence composition GI prediction methods (SIGI-HMM3 and IslandPath-DIMOB4) with IslandPick, the three most accurate methods known for predicting genomic islands.

New subcellular localization predictions based on PSORTb v.3.0 (manuscript in preparation). PSORTb v.3.0 can identify sub-category localizations in bacterial organelles and, for bacteria interacting with a host, differentiate proteins that are targeted to a host cell. The new version also exhibits higher sensitivity and genome prediction coverage compared to the previous version, with an average of 15% genome coverage increase for Gram-negative species.

Incorporation of computationally-predicted operons from the Database of Prokaryotic Operons (DOOR) into gene cards (example) and GBrowse (example).

Metabolic pathway data derived from the KEGG Metabolic Pathway Database has been integrated into the gene cards and the GBrowse view of external annotations. All pathways, including KEGG-derived pathways can be searched using the advanced Boolean search tool.

New ability to link to detailed gene pages using a GI number (e.g. http://www.burkholderia.com/getAnnotation.do?gi=107021570)

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