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] [-xdrop_ungap float_value]

    [-xdrop_gap float_value] [-xdrop_gap_final float_value]

    [-searchsp int_value] [-max_hsps_per_subject int_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] [-html] [-max_target_seqs num_sequences]

    [-num_threads int_value] [-remote] [-version]

DESCRIPTION

   Nucleotide-Nucleotide BLAST 2.2.26+

OPTIONAL ARGUMENTS

 -h

   Print USAGE and DESCRIPTION;  ignore other arguments

 -help

   Print USAGE, DESCRIPTION and ARGUMENTS description;  ignore other arguments

 -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

 -index_name <String>

   MegaBLAST database index name

 *** 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, 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

           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)

   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'

   Default = `0'

 -show_gis

   Show NCBI GIs in deflines?

 -num_descriptions <Integer, >=0>

   Number of database sequences to show one-line descriptions for

   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

 -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

 -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

    * 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

 -max_hsps_per_subject <Integer, >=0>

   Override maximum number of HSPs per subject to save for ungapped searches

   (0 means do not override)

   Default = `0'

 *** 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