The sequence obtained from the MASCOT database was analyzed with Glycomod [ 29], which is available at http://www.expasy.ch/tools/glycomod/.
Fluorescence images stored in an OMERO database were analyzed in Matlab with the following workflow: each m-by-n z stack (FITC channel) was downloaded into Matlab using the OMERO.matlab toolbox, and the resultant 3D matrix was reshaped into an m-by-n∗z plane to minimize edge effects.
ChIP-seq data sets from the Roadmap Epigenomics project deposited to GEO database were analyzed and converted to gene sets with the use of the tool SICER.
The unique genes from the catfish and the zebrafish annotated database were analyzed using generic GO-slim terms with Blast2GO [ 26, 27].
Data were entered in a centrally maintained database and were analyzed with Excel (Microsoft, Redmond, WA), SAS 8.0 (SAS, Cary, NC), and EpiInfo 6.2 software (5 ).
Surveillance data on yersiniosis, accessed through the national level database (SurvNet), were analyzed with regard to time trends, demographical and geographical distribution, serotypes, and hospitalization, for the time period 2001-2008.
Second, in order to assign names to the isolates not found in the SpolDB4 database, the spoligopatterns were analyzed with 'Spotclust', using a mixture model built on the SpolDB3 database [ 10].
All tRNA genes annotated in the L. major, T. brucei and T. cruzi genome databases (versions 2.1) were analyzed with the tRNAscan-SE program [ 43] to verify the presence and identity of the tRNAs.
Each new study that is to be loaded into the database is analyzed for compatibility with SDF.
The Surveillance, Epidemiology, and End Results (SEER) database was analyzed for patients with an H&N tumor site who were diagnosed between 2004 and 2011.
