option	type	default value	description and notes
db	string	none	BLAST database name.
query	string	stdin	Query file name.
query_loc	string	none	Location on the query sequence (Format: start-stop)
out	string	stdout	Output file name
evalue	real	10.0	Expect value (E) for saving hits
subject	string	none	File with subject sequence(s) to search.
subject_loc	string	none	Location on the subject sequence (Format: start-stop).
show_gis	flag	N/A	Show NCBI GIs in report.
num_descriptions	integer	500	Show one-line descriptions for this number of database sequences.
num_alignments	integer	250	Show alignments for this number of database sequences.
max_target_seqs	Integer	500	Number of aligned sequences to keep. Use with report formats that do not have separate definition line and alignment sections such as tabular (all outfmt > 4). Not compatible with num_descriptions or num_alignments.
max_hsps	integer	none	Maximum number of HSPs (alignments) to keep for any single query-subject pair. The HSPs shown will be the best as judged by expect value. This number should be an integer that is one or greater. If this option is not set, BLAST shows all HSPs meeting the expect value criteria. Setting it to one will show only the best HSP for every query-subject pair
html	flag	N/A	Produce HTML output
gilist	string	none	Restrict search of database to GI’s listed in this file. Local searches only.
negative_gilist	string	none	Restrict search of database to everything except the GI’s listed in this file. Local searches only.
entrez_query	string	none	Restrict search with the given Entrez query. Remote searches only.
culling_limit	integer	none	Delete a hit that is enveloped by at least this many higher-scoring hits.
best_hit_overhang	real	none	Best Hit algorithm overhang value (recommended value: 0.1)
best_hit_score_edge	real	none	Best Hit algorithm score edge value (recommended value: 0.1)
dbsize	integer	none	Effective size of the database
searchsp	integer	none	Effective length of the search space
import_search_strategy	string	none	Search strategy file to read.
export_search_strategy	string	none	Record search strategy to this file.
parse_deflines	flag	N/A	Parse query and subject bar delimited sequence identifiers (e.g., gi|129295).
num_threads	integer	1	Number of threads (CPUs) to use in blast search.
remote	flag	N/A	Execute search on NCBI servers?
outfmt	string	0	alignment view options: 0 = pairwise, 1 = query-anchored showing identities, 2 = query-anchored no identities, 3 = flat query-anchored, show identities, 4 = flat query-anchored, no identities, 5 = XML Blast output, 6 = tabular, 7 = tabular with comment lines, 8 = Text ASN.1, 9 = Binary ASN.1 10 = Comma-separated values 11 = BLAST archive format (ASN.1) Options 6, 7, and 10 can be additionally configured to produce a custom format specified by space delimited format specifiers. The supported format specifiers are: qseqid means Query Seq-id qgi means Query GI qacc means Query accesion sseqid means Subject Seq-id sallseqid means All subject Seq-id(s), separated by a ';' sgi means Subject GI sallgi means All subject GIs sacc means Subject accession sallacc means All subject accessions qstart means Start of alignment in query qend means End of alignment in query sstart means Start of alignment in subject send means End of alignment in subject qseq means Aligned part of query sequence sseq means Aligned part of subject sequence evalue means Expect value bitscore means Bit score score means Raw score length means Alignment length pident means Percentage of identical matches nident means Number of identical matches mismatch means Number of mismatches positive means Number of positive-scoring matches gapopen means Number of gap openings gaps means Total number of gap ppos means Percentage of positive-scoring matches frames means Query and subject frames separated by a '/' qframe means Query frame sframe means Subject frame btop means Blast traceback operations (BTOP) staxids means unique Subject Taxonomy ID(s), separated by a ';'(in numerical order) sscinames means unique Subject Scientific Name(s), separated by a ';' scomnames means unique Subject Common Name(s), separated by a ';' sblastnames means unique Subject Blast Name(s), separated by a ';' (in alphabetical order) sskingdoms means unique Subject Super Kingdom(s), separated by a ';' (in alphabetical order) stitle means Subject Title salltitles means All Subject Title(s), separated by a '<>' sstrand means Subject Strand qcovs means Query Coverage Per Subject (for all HSPs) qcovhsp means Query Coverage Per HSP qcovus is a measure of Query Coverage that counts a position in a subject sequence for this measure only once. The second time the position is aligned to the query is not counted towards this measure. When not provided, the default value is: 'qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore', which is equivalent to the keyword 'std'