Introducing to BLAST+ applications

USAGE    
  blastn [-h] [-help] [-import_search_strategy filename]    
    [-export_search_strategy filename] [-task task_name] [-db database_name]    
    [-dbsize num_letters] [-gilist filename] [-seqidlist filename]    
    [-negative_gilist filename] [-entrez_query entrez_query]    
    [-db_soft_mask filtering_algorithm] [-db_hard_mask filtering_algorithm]    
    [-subject subject_input_file] [-subject_loc range] [-query input_file]    
    [-out output_file] [-evalue evalue] [-word_size int_value]    
    [-gapopen open_penalty] [-gapextend extend_penalty]    
    [-perc_identity float_value] [-qcov_hsp_perc float_value]    
    [-max_hsps int_value] [-xdrop_ungap float_value] [-xdrop_gap float_value]    
    [-xdrop_gap_final float_value] [-searchsp int_value]    
    [-sum_stats bool_value] [-penalty penalty] [-reward reward] [-no_greedy]    
    [-min_raw_gapped_score int_value] [-template_type type]    
    [-template_length int_value] [-dust DUST_options]    
    [-filtering_db filtering_database]    
    [-window_masker_taxid window_masker_taxid]    
    [-window_masker_db window_masker_db] [-soft_masking soft_masking]    
    [-ungapped] [-culling_limit int_value] [-best_hit_overhang float_value]    
    [-best_hit_score_edge float_value] [-window_size int_value]    
    [-off_diagonal_range int_value] [-use_index boolean] [-index_name string]    
    [-lcase_masking] [-query_loc range] [-strand strand] [-parse_deflines]    
    [-outfmt format] [-show_gis] [-num_descriptions int_value]    
    [-num_alignments int_value] [-line_length line_length] [-html]    
    [-max_target_seqs num_sequences] [-num_threads int_value] [-remote]    
    [-version]    
    
DESCRIPTION    
   Nucleotide-Nucleotide BLAST 2.6.0+    
    
OPTIONAL ARGUMENTS    
 -h    
   Print USAGE and DESCRIPTION;  ignore all other parameters    
 -help    
   Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters    
 -version    
   Print version number;  ignore other arguments    
    
 *** Input query options    
 -query <File_In>    
   Input file name    
   Default = `-'    
 -query_loc <String>    
   Location on the query sequence in 1-based offsets (Format: start-stop)    
 -strand <String, `both', `minus', `plus'>    
   Query strand(s) to search against database/subject    
   Default = `both'    
    
 *** General search options    
 -task <String, Permissible values: 'blastn' 'blastn-short' 'dc-megablast'    
                'megablast' 'rmblastn' >    
   Task to execute    
   Default = `megablast'    
 -db <String>    
   BLAST database name    
    * Incompatible with:  subject, subject_loc    
 -out <File_Out>    
   Output file name    
   Default = `-'    
 -evalue <Real>    
   Expectation value (E) threshold for saving hits     
   Default = `10'    
 -word_size <Integer, >=4>    
   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'    
 -index_name <String>    
   MegaBLAST database index name (deprecated; use only for old style indices)    
    
 *** BLAST-2-Sequences options    
 -subject <File_In>    
   Subject sequence(s) to search    
    * Incompatible with:  db, gilist, seqidlist, negative_gilist,    
   db_soft_mask, db_hard_mask    
 -subject_loc <String>    
   Location on the subject sequence in 1-based offsets (Format: start-stop)    
    * Incompatible with:  db, gilist, seqidlist, negative_gilist,    
   db_soft_mask, db_hard_mask, remote    
    
 *** Formatting options    
 -outfmt <String>    
   alignment view options:    
     0 = Pairwise,    
     1 = Query-anchored showing identities,    
     2 = Query-anchored no identities,    
     3 = Flat query-anchored showing identities,    
     4 = Flat query-anchored no identities,    
     5 = BLAST XML,    
     6 = Tabular,    
     7 = Tabular with comment lines,    
     8 = Seqalign (Text ASN.1),    
     9 = Seqalign (Binary ASN.1),    
    10 = Comma-separated values,    
    11 = BLAST archive (ASN.1),    
    12 = Seqalign (JSON),    
    13 = Multiple-file BLAST JSON,    
    14 = Multiple-file BLAST XML2,    
    15 = Single-file BLAST JSON,    
    16 = Single-file BLAST XML2,    
    17 = Sequence Alignment/Map (SAM),    
    18 = Organism Report    
       
   Options 6, 7, 10 and 17 can be additionally configured to produce    
   a custom format specified by space delimited format specifiers.    
   The supported format specifiers for options 6, 7 and 10 are:    
   	    qseqid means Query Seq-id    
   	       qgi means Query GI    
   	      qacc means Query accesion    
   	   qaccver means Query accesion.version    
   	      qlen means Query sequence length    
   	    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    
   	   saccver means Subject accession.version    
   	   sallacc means All subject accessions    
   	      slen means Subject sequence length    
   	    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 gaps    
   	      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)    
   	    staxid means Subject Taxonomy ID    
   	  ssciname means Subject Scientific Name    
   	  scomname means Subject Common Name    
   	sblastname means Subject Blast Name    
   	 sskingdom means Subject Super Kingdom    
   	   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    
   	   qcovhsp means Query Coverage Per HSP    
   	    qcovus means Query Coverage Per Unique Subject (blastn only)    
   When not provided, the default value is:    
   'qaccver saccver pident length mismatch gapopen qstart qend sstart send    
   evalue bitscore', which is equivalent to the keyword 'std'    
   The supported format specifier for option 17 is:    
   	        SQ means Include Sequence Data    
   	        SR means Subject as Reference Seq    
   Default = `0'    
 -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'    
 -html    
   Produce HTML output?    
    
 *** Query filtering options    
 -dust <String>    
   Filter query sequence with DUST (Format: 'yes', 'level window linker', or    
   'no' to disable)    
   Default = `20 64 1'    
 -filtering_db <String>    
   BLAST database containing filtering elements (i.e.: repeats)    
 -window_masker_taxid <Integer>    
   Enable WindowMasker filtering using a Taxonomic ID    
 -window_masker_db <String>    
   Enable WindowMasker filtering using this repeats database.    
 -soft_masking <Boolean>    
   Apply filtering locations as soft masks    
   Default = `true'    
 -lcase_masking    
   Use lower case filtering in query and subject sequence(s)?    
    
 *** Restrict search or results    
 -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:  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    
 -max_target_seqs <Integer, >=1>    
   Maximum number of aligned sequences to keep     
   Not applicable for outfmt <= 4    
   Default = `500'    
    * Incompatible with:  num_descriptions, num_alignments    
    
 *** Discontiguous MegaBLAST options    
 -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    
    
 *** Statistical options    
 -dbsize <Int8>    
   Effective length of the database     
 -searchsp <Int8, >=0>    
   Effective length of the search space    
 -sum_stats <Boolean>    
   Use sum statistics    
    
 *** Search strategy options    
 -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    
    
 *** Extension options    
 -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'    
    
 *** Miscellaneous options    
 -parse_deflines    
   Should the query and subject defline(s) be parsed?    
 -num_threads <Integer, >=1>    
   Number of threads (CPUs) to use in the BLAST search    
   Default = `1'    
    * Incompatible with:  remote    
 -remote    
   Execute search remotely?    
    * Incompatible with:  gilist, seqidlist, negative_gilist, subject_loc,    
   num_threads