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-evalue <Real> Expectation value (E) threshold for saving hits Default = '10'
-word_size <Integer, >=2> Word size for wordfinder algorithm
-gapopen <Integer> Cost to open a gap
-gapextend <Integer> Cost to extend a gap
-matrix <String> Scoring matrix name (normally BLOSUM62)
-threshold <Real, >=0> Minimum word score such that the word is added to the BLAST lookup table
-comp_based_stats <String> Use composition-based statistics for blastp / tblastn: D or d: default (equivalent to 2) 0 or F or f: no composition-based statistics 1: Composition-based statistics as in NAR 29:2994-3005, 2001 2 or T or t : Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties 3: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally For programs other than tblastn, must either be absent or be D, F or 0 Default = `2'
-num_descriptions <Integer, >=0> Number of database sequences to show one-line descriptions for Default = `500'
-num_alignments <Integer, >=0> Number of database sequences to show alignments for Default = `250'
-seg <String> Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or 'no' to disable) Default = `no'
-soft_masking <Boolean> Apply filtering locations as soft masks Default = `false'
-lcase_masking Use lower case filtering in query and subject sequence(s)?
-gilist <String> Restrict search of database to list of GI's * Incompatible with: negative_gilist, seqidlist, remote, subject, subject_loc
-seqidlist <String> Restrict search of database to list of SeqId's * Incompatible with: gilist, negative_gilist, remote, subject, subject_loc
-negative_gilist <String> Restrict search of database to everything except the listed GIs * Incompatible with: gilist, seqidlist, remote, subject, subject_loc
-entrez_query <String> Restrict search with the given Entrez query * Requires: remote
-db_soft_mask <String> Filtering algorithm ID to apply to the BLAST database as soft masking * Incompatible with: subject, subject_loc
-culling_limit <Integer, >=0> If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit * Incompatible with: best_hit_overhang, best_hit_score_edge
-best_hit_overhang <Real, (>0 and <0.5)> Best Hit algorithm overhang value (recommended value: 0.1) * Incompatible with: culling_limit
-best_hit_score_edge <Real, (>0 and <0.5)> Best Hit algorithm score edge value (recommended value: 0.1) * Incompatible with: culling_limit
-max_target_seqs <Integer, >=1> Maximum number of aligned sequences to keep
This could take some time depending on the size of your query and database(s).