Blastx - searches a nucleotide query sequence translated in all reading frames against a protein database. Tblastn - searches a protein query sequence against a dynamically translated nucleotide database. There are also search options that can be specified for the sensitivity of the search, though in most case the default options are sufficient. The user is directed to the NCBI help pages for information on the setting of these parameters. Downloading updated databases from the NCBI's FTP site is done overnight on a daily basis.
Tools exist to support and format user developed databases.
Once an input sequence is specified along with the program and database, the user need only select the search button. The page will be completed once the search is finished. The output window has a graphical display of the distribution of hits found, along with a listing of the hits with significant alignments and links to the matching sequences' Entrez entries. Statistical information about the search and information on the date and size of the database are found at the end of the output window. NWChem Updates by Anita Orendt, Molecular Sciences, CHPC NWChem 4.0 is now installed on raptor and installation on icebox should follow shortly.