DGENE, USGENE, and PCTGEN: STN biosequence searches with enhanced performance
FIZ Karlsruhe has enhanced the performance for biosequence searches in the databases DGENE (GENESEQTM) , USGENE (USPTO Genetic Sequence Database), and PCTGEN (World Patent Application Biosequences). Searches (RUN GETSEQ, RUN GETSIM, RUN BLAST, BATCH search) now run in a fraction of the time you have been used to.
The BLAST suite of programs has been upgraded to a newer version. mpiBLAST 1.5.0. is being used to achieve these considerable performance gains. For more information about the program, please visit: http://www.mpiblast.org/.
Since mpiBLAST 1.5.0. uses the more recent BLAST version 2.2.15 new parameter options become available.
For more detailed information on the BLAST algorithm consult the NCBI documentation at: http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs
The online helps containing information on the BLAST program, parameter settings, default and valid values, etc. have been updated. Please see HELP OPTIONS and HELP NCBI.
The general default options and search behavior have not changed. Thus, you should not see noticeable changes to your search results when using default parameters. However, the range of accepted values may have changed.
Please note that although now running faster, the underlying program versions for the GETSEQ and GETSIM searches have not changed.