Sequence similarity search (BLAST) against the UAMH culture collection
-task <String, Permissible values: 'tblastn' 'tblastn-fast'> Task to execute Default = 'tblastn'
-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
-db_gencode <Integer, values between: 1-6, 9-16, 21-31, 33> Genetic code to use to translate database/subjects (see user manual for details) Default = '1'
-max_intron_length <Integer, >=0> Length of the largest intron allowed in a translated nucleotide sequence when linking multiple distinct alignments Default = '0'
-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'
-show_gis Show NCBI GIs in deflines?
-num_descriptions <Integer, >=0> Number of database sequences to show one-line descriptions for Not applicable for outfmt > 4 Default = '500' * Incompatible with: max_target_seqs
-num_alignments <Integer, >=0> Number of database sequences to show alignments for Default = '250' * Incompatible with: max_target_seqs
-seg <String> Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or 'no' to disable) Default = '12 2.2 2.5'
-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 GIs * Incompatible with: seqidlist, taxids, taxidlist, negative_gilist, negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject, subject_loc
-seqidlist <String> Restrict search of database to list of SeqIDs * Incompatible with: gilist, taxids, taxidlist, negative_gilist, negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject, subject_loc
-negative_gilist <String> Restrict search of database to everything except the specified GIs * Incompatible with: gilist, seqidlist, taxids, taxidlist, negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject, subject_loc
-negative_seqidlist <String> Restrict search of database to everything except the specified SeqIDs * Incompatible with: gilist, seqidlist, taxids, taxidlist, negative_gilist, negative_taxids, negative_taxidlist, remote, subject, subject_loc
-taxids <String> Restrict search of database to include only the specified taxonomy IDs (multiple IDs delimited by ',') * Incompatible with: gilist, seqidlist, taxidlist, negative_gilist, negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject, subject_loc
-negative_taxids <String> Restrict search of database to everything except the specified taxonomy IDs (multiple IDs delimited by ',') * Incompatible with: gilist, seqidlist, taxids, taxidlist, negative_gilist, negative_seqidlist, negative_taxidlist, remote, subject, subject_loc
-taxidlist <String> Restrict search of database to include only the specified taxonomy IDs * Incompatible with: gilist, seqidlist, taxids, negative_gilist, negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject, subject_loc
-negative_taxidlist <String> Restrict search of database to everything except the specified taxonomy IDs * Incompatible with: gilist, seqidlist, taxids, taxidlist, negative_gilist, negative_seqidlist, negative_taxids, 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: db_hard_mask, subject, subject_loc
-db_hard_mask <String> Filtering algorithm ID to apply to the BLAST database as hard masking * Incompatible with: db_soft_mask, subject, subject_loc
-qcov_hsp_perc <Real, 0..100> Percent query coverage per hsp
-max_hsps <Integer, >=1> Set maximum number of HSPs per subject sequence to save for each query
-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
-subject_besthit Turn on best hit per subject sequence
-max_target_seqs <Integer, >=1> Maximum number of aligned sequences to keep (value of 5 or more is recommended) Default = '500' * Incompatible with: num_descriptions, num_alignments
-dbsize <Int8> Effective length of the database
-searchsp <Int8, >=0> Effective length of the search space
-sum_stats <Boolean> Use sum statistics
-xdrop_ungap <Real> X-dropoff value (in bits) for ungapped extensions
-xdrop_gap <Real> X-dropoff value (in bits) for preliminary gapped extensions
-xdrop_gap_final <Real> X-dropoff value (in bits) for final gapped alignment
-ungapped Perform ungapped alignment only?
-window_size <Integer, >=0> Multiple hits window size, use 0 to specify 1-hit algorithm
-task <String, Permissible values: 'blastn' 'blastn-short' 'dc-megablast' 'megablast' 'rmblastn'> Task to execute Default = 'megablast'
-evalue <Real> Expectation value (E) threshold for saving hits Default = '10' (1000 for blastn-short)
-word_size <Integer, >=2> Word size for wordfinder algorithm (length of best perfect match)
-gapopen <Integer> Cost to open a gap
-gapextend <Integer> Cost to extend a gap
-penalty <Integer, <=0> Penalty for a nucleotide mismatch
-reward <Integer, >=0> Reward for a nucleotide match
-use_index <Boolean> Use MegaBLAST database index Default = 'false'
-show_gis Show NCBI GIs in deflines?
-num_descriptions <Integer, >=0> Number of database sequences to show one-line descriptions for Not applicable for outfmt > 4 Default = '500' * Incompatible with: max_target_seqs
-num_alignments <Integer, >=0> Number of database sequences to show alignments for Default = '250' * Incompatible with: max_target_seqs
-line_length <Integer, >=1> Line length for formatting alignments Not applicable for outfmt > 4 Default = '60'
-dust <String>
Filter query sequence with DUST (Format: 'yes', 'level window linker', or
'no' to disable)
Default = '20 64 1' ('no' for blastn-short)
-soft_masking <Boolean> Apply filtering locations as soft masks Default = 'true'
-lcase_masking Use lower case filtering in query and subject sequence(s)?
-gilist <String> Restrict search of database to list of GIs * Incompatible with: seqidlist, taxids, taxidlist, negative_gilist, negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject, subject_loc
-seqidlist <String> Restrict search of database to list of SeqIDs * Incompatible with: gilist, taxids, taxidlist, negative_gilist, negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject, subject_loc
-negative_gilist <String> Restrict search of database to everything except the specified GIs * Incompatible with: gilist, seqidlist, taxids, taxidlist, negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject, subject_loc
-negative_seqidlist <String> Restrict search of database to everything except the specified SeqIDs * Incompatible with: gilist, seqidlist, taxids, taxidlist, negative_gilist, negative_taxids, negative_taxidlist, remote, subject, subject_loc
-taxids <String> Restrict search of database to include only the specified taxonomy IDs (multiple IDs delimited by ',') * Incompatible with: gilist, seqidlist, taxidlist, negative_gilist, negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject, subject_loc
-negative_taxids <String> Restrict search of database to everything except the specified taxonomy IDs (multiple IDs delimited by ',') * Incompatible with: gilist, seqidlist, taxids, taxidlist, negative_gilist, negative_seqidlist, negative_taxidlist, remote, subject, subject_loc
-taxidlist <String> Restrict search of database to include only the specified taxonomy IDs * Incompatible with: gilist, seqidlist, taxids, negative_gilist, negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject, subject_loc
-negative_taxidlist <String> Restrict search of database to everything except the specified taxonomy IDs * Incompatible with: gilist, seqidlist, taxids, taxidlist, negative_gilist, negative_seqidlist, negative_taxids, 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: db_hard_mask, subject, subject_loc
-db_hard_mask <String> Filtering algorithm ID to apply to the BLAST database as hard masking * Incompatible with: db_soft_mask, subject, subject_loc
-perc_identity <Real, 0..100> Percent identity
-qcov_hsp_perc <Real, 0..100> Percent query coverage per hsp
-max_hsps <Integer, >=1> Set maximum number of HSPs per subject sequence to save for each query
-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
-subject_besthit Turn on best hit per subject sequence
-max_target_seqs <Integer, >=1> Maximum number of aligned sequences to keep (value of 5 or more is recommended) Default = '500' * Incompatible with: num_descriptions, num_alignments
-template_type <String, `coding', `coding_and_optimal', `optimal'> Discontiguous MegaBLAST template type * Requires: template_length
-template_length <Integer, Permissible values: '16' '18' '21' > Discontiguous MegaBLAST template length * Requires: template_type
-dbsize <Int8> Effective length of the database
-searchsp <Int8, >=0> Effective length of the search space
-xdrop_ungap <Real> X-dropoff value (in bits) for ungapped extensions
-xdrop_gap <Real> X-dropoff value (in bits) for preliminary gapped extensions
-xdrop_gap_final <Real> X-dropoff value (in bits) for final gapped alignment
-no_greedy Use non-greedy dynamic programming extension
-min_raw_gapped_score <Integer> Minimum raw gapped score to keep an alignment in the preliminary gapped and traceback stages
-ungapped Perform ungapped alignment only?
-window_size <Integer, >=0> Multiple hits window size, use 0 to specify 1-hit algorithm
-off_diagonal_range <Integer, >=0> Number of off-diagonals to search for the 2nd hit, use 0 to turn off Default = `0'
-parse_deflines <Real> Should the query and subject defline(s) be parsed?
-strand <String, `both', `minus', `plus'> Query strand(s) to search against database/subject Default = 'both'
-query_gencode <Integer, values between: 1-6, 9-16, 21-31, 33> Genetic code to use to translate query (see https://www.ncbi.nlm.nih.gov/Taxonomy/ taxonomyhome.html/index.cgi?chapter=cgencodes for details) Default = '1'
-task <String, Permissible values: 'blastx' 'blastx-fast'> Task to execute Default = 'blastx'
-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
-max_intron_length <Integer, >=0> Length of the largest intron allowed in a translated nucleotide sequence when linking multiple distinct alignments Default = '0'
-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:
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
Default = '2'
-show_gis Show NCBI GIs in deflines?
-num_descriptions <Integer, >=0> Number of database sequences to show one-line descriptions for Not applicable for outfmt > 4 Default = '500' * Incompatible with: max_target_seqs
-num_alignments <Integer, >=0> Number of database sequences to show alignments for Default = '250' * Incompatible with: max_target_seqs
-sorthits <Integer, (>=0 and =<4)>
Sorting option for hits:
alignment view options:
0 = Sort by evalue,
1 = Sort by bit score,
2 = Sort by total score,
3 = Sort by percent identity,
4 = Sort by query coverage
Not applicable for outfmt > 4
-sorthsps <Integer, (>=0 and =<4)>
Sorting option for hps:
0 = Sort by hsp evalue,
1 = Sort by hsp score,
2 = Sort by hsp query start,
3 = Sort by hsp percent identity,
4 = Sort by hsp subject start
Not applicable for outfmt != 0
-seg <String> Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or 'no' to disable) Default = '12 2.2 2.5'
-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 GIs * Incompatible with: seqidlist, taxids, taxidlist, negative_gilist, negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject, subject_loc
-seqidlist <String> Restrict search of database to list of SeqIDs * Incompatible with: gilist, taxids, taxidlist, negative_gilist, negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject, subject_loc
-negative_gilist <String> Restrict search of database to everything except the specified GIs * Incompatible with: gilist, seqidlist, taxids, taxidlist, negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject, subject_loc
-negative_seqidlist <String> Restrict search of database to everything except the specified SeqIDs * Incompatible with: gilist, seqidlist, taxids, taxidlist, negative_gilist, negative_taxids, negative_taxidlist, remote, subject, subject_loc
-taxids <String> Restrict search of database to include only the specified taxonomy IDs (multiple IDs delimited by ',') * Incompatible with: gilist, seqidlist, taxidlist, negative_gilist, negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject, subject_loc
-negative_taxids <String> Restrict search of database to everything except the specified taxonomy IDs (multiple IDs delimited by ',') * Incompatible with: gilist, seqidlist, taxids, taxidlist, negative_gilist, negative_seqidlist, negative_taxidlist, remote, subject, subject_loc
-taxidlist <String> Restrict search of database to include only the specified taxonomy IDs * Incompatible with: gilist, seqidlist, taxids, negative_gilist, negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject, subject_loc
-negative_taxidlist <String> Restrict search of database to everything except the specified taxonomy IDs * Incompatible with: gilist, seqidlist, taxids, taxidlist, negative_gilist, negative_seqidlist, negative_taxids, remote, subject, subject_loc
-ipglist <String> Restrict search of database to list of IPGs * Incompatible with: subject, subject_loc
-negative_ipglist <String> Restrict search of database to everything except the specified IPGs * Incompatible with: 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: db_hard_mask, subject, subject_loc
-db_hard_mask <String> Filtering algorithm ID to apply to the BLAST database as hard masking * Incompatible with: db_soft_mask, subject, subject_loc
-qcov_hsp_perc <Real, 0..100> Percent query coverage per hsp
-max_hsps <Integer, >=1> Set maximum number of HSPs per subject sequence to save for each query
-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
-subject_besthit Turn on best hit per subject sequence
-max_target_seqs <Integer, >=1> Maximum number of aligned sequences to keep (value of 5 or more is recommended) Default = '500' * Incompatible with: num_descriptions, num_alignments
-dbsize <Int8> Effective length of the database
-searchsp <Int8, >=0> Effective length of the search space
-sum_stats <Boolean> Use sum statistics
-xdrop_ungap <Real> X-dropoff value (in bits) for ungapped extensions
-xdrop_gap <Real> X-dropoff value (in bits) for preliminary gapped extensions
-xdrop_gap_final <Real> X-dropoff value (in bits) for final gapped alignment
-window_size <Integer, >=0> Multiple hits window size, use 0 to specify 1-hit algorithm
-ungapped Perform ungapped alignment only?
-parse_deflines <Real> Should the query and subject defline(s) be parsed?
-use_sw_tback <Real> Compute locally optimal Smith-Waterman alignments?
-strand <String, `both', `minus', `plus'> Query strand(s) to search against database/subject Default = 'both'
-query_gencode <Integer, values between: 1-6, 9-16, 21-31, 33> Genetic code to use to translate query (see https://www.ncbi.nlm.nih.gov/Taxonomy/ taxonomyhome.html/index.cgi?chapter=cgencodes for details) Default = '1'
-evalue <Real> Expectation value (E) threshold for saving hits Default = '10'
-word_size <Integer, >=2> Word size for wordfinder algorithm
-max_intron_length <Integer, >=0> Length of the largest intron allowed in a translated nucleotide sequence when linking multiple distinct alignments Default = '0'
-matrix <String> Scoring matrix name (normally BLOSUM62)
-threshold <Real, >=0> Minimum word score such that the word is added to the BLAST lookup table
-db_gencode <Integer, values between: 1-6, 9-16, 21-31, 33> Genetic code to use to translate database/subjects (see user manual for details) Default = '1'
-show_gis Show NCBI GIs in deflines?
-num_descriptions <Integer, >=0> Number of database sequences to show one-line descriptions for Not applicable for outfmt > 4 Default = '500' * Incompatible with: max_target_seqs
-num_alignments <Integer, >=0> Number of database sequences to show alignments for Default = '250' * Incompatible with: max_target_seqs
-sorthits <Integer, (>=0 and =<4)>
Sorting option for hits:
alignment view options:
0 = Sort by evalue,
1 = Sort by bit score,
2 = Sort by total score,
3 = Sort by percent identity,
4 = Sort by query coverage
Not applicable for outfmt > 4
-sorthsps <Integer, (>=0 and =<4)>
Sorting option for hps:
0 = Sort by hsp evalue,
1 = Sort by hsp score,
2 = Sort by hsp query start,
3 = Sort by hsp percent identity,
4 = Sort by hsp subject start
Not applicable for outfmt != 0
-seg <String> Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or 'no' to disable) Default = '12 2.2 2.5'
-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 GIs * Incompatible with: seqidlist, taxids, taxidlist, negative_gilist, negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject, subject_loc
-seqidlist <String> Restrict search of database to list of SeqIDs * Incompatible with: gilist, taxids, taxidlist, negative_gilist, negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject, subject_loc
-negative_gilist <String> Restrict search of database to everything except the specified GIs * Incompatible with: gilist, seqidlist, taxids, taxidlist, negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject, subject_loc
-negative_seqidlist <String> Restrict search of database to everything except the specified SeqIDs * Incompatible with: gilist, seqidlist, taxids, taxidlist, negative_gilist, negative_taxids, negative_taxidlist, remote, subject, subject_loc
-taxids <String> Restrict search of database to include only the specified taxonomy IDs (multiple IDs delimited by ',') * Incompatible with: gilist, seqidlist, taxidlist, negative_gilist, negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject, subject_loc
-negative_taxids <String> Restrict search of database to everything except the specified taxonomy IDs (multiple IDs delimited by ',') * Incompatible with: gilist, seqidlist, taxids, taxidlist, negative_gilist, negative_seqidlist, negative_taxidlist, remote, subject, subject_loc
-taxidlist <String> Restrict search of database to include only the specified taxonomy IDs * Incompatible with: gilist, seqidlist, taxids, negative_gilist, negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject, subject_loc
-negative_taxidlist <String> Restrict search of database to everything except the specified taxonomy IDs * Incompatible with: gilist, seqidlist, taxids, taxidlist, negative_gilist, negative_seqidlist, negative_taxids, 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: db_hard_mask, subject, subject_loc
-db_hard_mask <String> Filtering algorithm ID to apply to the BLAST database as hard masking * Incompatible with: db_soft_mask, subject, subject_loc
-qcov_hsp_perc <Real, 0..100> Percent query coverage per hsp
-max_hsps <Integer, >=1> Set maximum number of HSPs per subject sequence to save for each query
-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
-subject_besthit Turn on best hit per subject sequence
-max_target_seqs <Integer, >=1> Maximum number of aligned sequences to keep (value of 5 or more is recommended) Default = '500' * Incompatible with: num_descriptions, num_alignments
-dbsize <Int8> Effective length of the database
-searchsp <Int8, >=0> Effective length of the search space
-sum_stats <Boolean> Use sum statistics
-import_search_strategy <File_In> Search strategy to use * Incompatible with: export_search_strategy
-export_search_strategy <File_Out> File name to record the search strategy used * Incompatible with: import_search_strategy
-sum_stats <Boolean> Use sum statistics
-xdrop_ungap <Real> X-dropoff value (in bits) for ungapped extensions
-window_size <Integer, >=0> Multiple hits window size, use 0 to specify 1-hit algorithm
-parse_deflines <Real> Should the query and subject defline(s) be parsed?
-task <String, Permissible values: 'blastp' 'blastp-fast' 'blastp-short'> Task to execute Default = 'blastp'
-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:
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
Default = '2'
-num_descriptions <Integer, >=0> Number of database sequences to show one-line descriptions for Not applicable for outfmt > 4 Default = '500' * Incompatible with: max_target_seqs
-num_alignments <Integer, >=0> Number of database sequences to show alignments for Default = '250' * Incompatible with: max_target_seqs
-sorthits <Integer, (>=0 and =<4)>
Sorting option for hits:
alignment view options:
0 = Sort by evalue,
1 = Sort by bit score,
2 = Sort by total score,
3 = Sort by percent identity,
4 = Sort by query coverage
Not applicable for outfmt > 4
-sorthsps <Integer, (>=0 and =<4)>
Sorting option for hps:
0 = Sort by hsp evalue,
1 = Sort by hsp score,
2 = Sort by hsp query start,
3 = Sort by hsp percent identity,
4 = Sort by hsp subject start
Not applicable for outfmt != 0
-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 GIs * Incompatible with: seqidlist, taxids, taxidlist, negative_gilist, negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject, subject_loc
-seqidlist <String> Restrict search of database to list of SeqIDs * Incompatible with: gilist, taxids, taxidlist, negative_gilist, negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject, subject_loc
-negative_gilist <String> Restrict search of database to everything except the specified GIs * Incompatible with: gilist, seqidlist, taxids, taxidlist, negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject, subject_loc
-negative_seqidlist <String> Restrict search of database to everything except the specified SeqIDs * Incompatible with: gilist, seqidlist, taxids, taxidlist, negative_gilist, negative_taxids, negative_taxidlist, remote, subject, subject_loc
-taxids <String> Restrict search of database to include only the specified taxonomy IDs (multiple IDs delimited by ',') * Incompatible with: gilist, seqidlist, taxidlist, negative_gilist, negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject, subject_loc
-negative_taxids <String> Restrict search of database to everything except the specified taxonomy IDs (multiple IDs delimited by ',') * Incompatible with: gilist, seqidlist, taxids, taxidlist, negative_gilist, negative_seqidlist, negative_taxidlist, remote, subject, subject_loc
-taxidlist <String> Restrict search of database to include only the specified taxonomy IDs * Incompatible with: gilist, seqidlist, taxids, negative_gilist, negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject, subject_loc
-negative_taxidlist <String> Restrict search of database to everything except the specified taxonomy IDs * Incompatible with: gilist, seqidlist, taxids, taxidlist, negative_gilist, negative_seqidlist, negative_taxids, remote, subject, subject_loc
-ipglist <String> Restrict search of database to list of IPGs * Incompatible with: subject, subject_loc
-negative_ipglist <String> Restrict search of database to everything except the specified IPGs * Incompatible with: 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: db_hard_mask, subject, subject_loc
-db_hard_mask <String> Filtering algorithm ID to apply to the BLAST database as hard masking * Incompatible with: db_soft_mask, subject, subject_loc
-qcov_hsp_perc <Real, 0..100> Percent query coverage per hsp
-max_hsps <Integer, >=1> Set maximum number of HSPs per subject sequence to save for each query
-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
-subject_besthit Turn on best hit per subject sequence
-max_target_seqs <Integer, >=1> Maximum number of aligned sequences to keep (value of 5 or more is recommended) Default = '500' * Incompatible with: num_descriptions, num_alignments
-dbsize <Int8> Effective length of the database
-searchsp <Int8, >=0> Effective length of the search space
-xdrop_ungap <Real> X-dropoff value (in bits) for ungapped extensions
-xdrop_gap <Real> X-dropoff value (in bits) for preliminary gapped extensions
-xdrop_gap_final <Real> X-dropoff value (in bits) for final gapped alignment
-window_size <Integer, >=0> Multiple hits window size, use 0 to specify 1-hit algorithm
-ungapped Perform ungapped alignment only?
-parse_deflines <Real> Should the query and subject defline(s) be parsed?
-use_sw_tback <Real> Compute locally optimal Smith-Waterman alignments?