The ENTREZ_QUERY and FORMAT_ENTREZ_QUERY parameters requires valid Entrez query terms linked by appropriate Boolean operators (NOT, AND, OR). Boolean operators CANNOT be placed at the begining of the input. For example, 'NOT biomol_rna[prop]' will not work. To exclude entries, we will need to retrieve a meaningful set first. The example query terms below retrieve the complete set first before excluding the genomic records from the set:
all[filter] NOT biomol_genomic[prop]
The ENTREZ_QUERY parameter works in the 'Put' step to limit a BLAST search to the subset of the database sequences specified by the GI list. While FORMAT_ENTREZ_QUERY works in the 'Get' step to limit the result display to sequences that match the Entrez query without affecting the BLAST result saved by BLAST server. In other words, FORMAT_ENTREZ_QUERY works in a post search manner. We can get the all the alignments saved by BLAST by reformatting the result without using FORMAT_ENTREZ_QUERY.
When deciding what Entrez query terms to use for a given search, we need to take the database content into consideration. For example, applying the Entrez query term 'biomol_mrna[prop]' to the htgs database will not work since this database contains no mRNA entries at all. For more information on database contents, please refer to:
http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastdb.html
More information on Entrez query terms is available in Entrez Help Document located at:
http://www.ncbi.nlm.nih.gov/entrez/query/static/help/helpdoc.html
Only the ENTREZ_QUERY parameter is available to the client server version of wwwblast. A partially equivalent parameter in commandline BLAST is '-l', which only affects the search and takes a file with a list of gi as input. More information is available at:
http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastall/blastall_node53.html