Blast+

总是记不住blast的参数设置，现在把参数及用法放在此处，方便以后查阅~

Nucleotide-NucleotideBLAST 2.2.28+ usage   blastn [-h] [-help] [-import_search_strategyfilename]     [-export_search_strategy filename] [-tasktask_name] [-db database_name]     [-dbsize num_letters] [-gilist filename][-seqidlist filename]     [-negative_gilist filename] [-entrez_queryentrez_query]     [-db_soft_mask filtering_algorithm][-db_hard_mask filtering_algorithm]     [-subjectsubject_input_file] [-subject_loc range] [-query input_file]     [-outoutput_file] [-evalueevalue] [-word_size int_value]     [-gapopen open_penalty] [-gapextendextend_penalty]    [-perc_identity float_value] [-xdrop_ungapfloat_value]     [-xdrop_gap float_value] [-xdrop_gap_finalfloat_value]     [-searchsp int_value] [-max_hsps_per_subjectint_value] [-penalty penalty]     [-reward reward] [-no_greedy][-min_raw_gapped_score int_value]     [-template_type type] [-template_lengthint_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_overhangfloat_value]     [-best_hit_score_edge float_value][-window_size int_value]     [-off_diagonal_range int_value] [-use_indexboolean] [-index_name string]     [-lcase_masking] [-query_loc range] [-strandstrand] [-parse_deflines]     [-outfmt format] [-show_gis] [-num_descriptionsint_value]     [-num_alignments int_value] [-html][-max_target_seqs num_sequences]     [-num_threadsint_value] [-remote] [-version] OPTIONAL ARGUMENTS  -h    Print USAGE and DESCRIPTION;  ignore allother parameters  -help    Print USAGE, DESCRIPTION and ARGUMENTS; ignoreall other parameters  -version    Print version number;  ignore otherarguments  *** Input query options  -query    Input file name    Default = `-'  -query_loc    Location on the query sequence in 1-based offsets(Format: start-stop)  -strand    Query strand(s) to search againstdatabase/subject    Default = `both'  *** General search options  -task        'megablast' 'rmblastn' >    Task to execute    Default = `megablast'  -db    BLAST database name     * Incompatible with:  subject,subject_loc  -out    Output file name    Default = `-'  -evalue    Expectation value (E) threshold for savinghits     Default = `10'  -word_size =4>    Word size for wordfinder algorithm (length ofbest perfect match)  -gapopen    Cost to open a gap  -gapextend    Cost to extend a gap  -penalty    Penalty for a nucleotide mismatch  -reward =0>    Reward for a nucleotide match  -use_index    Use MegaBLAST database index  -index_name    MegaBLAST database index name  *** BLAST-2-Sequences options  -subject    Subject sequence(s) to search     * Incompatible with:  db, gilist,seqidlist, negative_gilist,    db_soft_mask, db_hard_mask  -subject_loc    Location on the subject sequence in 1-basedoffsets (Format: start-stop)     * Incompatible with:  db, gilist,seqidlist, negative_gilist,    db_soft_mask, db_hard_mask, remote  *** Formatting options  -outfmt    alignment view options:      0 = pairwise,      1 = query-anchored showingidentities,      2 = query-anchored no identities,      3 = flat query-anchored, showidentities,      4 = flat query-anchored, noidentities,      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 additionallyconfigured to produce    a custom format specified by space delimitedformat specifiers.    The supported format specifiers are:       qseqid means Query Seq-id             qgi means Query GI          qacc means Queryaccesion     qaccver means Queryaccesion.version           qlen means Query sequencelength        sseqid means Subject Seq-id    sallseqid means All subject Seq-id(s), separatedby a ';'             sgi means Subject GI         sallgi means All subject GIs          sacc means Subjectaccession     saccver means Subjectaccession.version      sallacc means All subjectaccessions          slen means Subject sequencelength        qstart means Start of alignment inquery          qend means End of alignmentin query         sstart means Start of alignment insubject          send means End of alignmentin subject          qseq means Aligned part ofquery sequence          sseq means Aligned part ofsubject sequence       evalue means Expect value     bitscore means Bit score         score means Raw score        length means Alignment length        pident means Percentage ofidentical matches        nident means Number of identicalmatches   mismatch means Number of mismatches      positive means Number of positive-scoringmatches    gapopen means Number of gapopenings          gaps means Total number ofgaps          ppos means Percentage ofpositive-scoring matches       frames means Query and subjectframes separated by a '/'       qframe means Query frame       sframe means Subject frame           btop means Blast tracebackoperations (BTOP)       staxids means Subject Taxonomy ID(s),separated by a ';' sscinames means Subject Scientific Name(s),separated by a ';  scomnames means Subject Common Name(s),separated by a ';'    sblastnames means Subject Blast Name(s),separated by a ';'     (in alphabetical order)    sskingdoms means Subject Super Kingdom(s),separated by a ';'     (in alphabetical order)         stitle means Subject Title    salltitles means All Subject Title(s), separatedby a '<>'       sstrand means Subject Strand         qcovs means Query Coverage PerSubject       qcovhsp means Query Coverage PerHSP    When not provided, the default value is:    'qseqid sseqid pident length mismatch gapopenqstart qend sstart send    evalue bitscore', which is equivalent to thekeyword 'std'    Default = `0'  -show_gis    Show NCBI GIs in deflines?  -num_descriptions =0>    Number of database sequences to show one-linedescriptions for    Not applicable for outfmt > 4    Default = `500'     * Incompatible with:  max_target_seqs  -num_alignments =0>    Number of database sequences to show alignmentsfor    Default = `250'     * Incompatible with:  max_target_seqs  -html    Produce HTML output?  *** Query filtering options  -dust    Filter query sequence with DUST (Format: 'yes','level window linker', or    'no' to disable)    Default = `20 64 1'  -filtering_db    BLAST database containing filtering elements(i.e.: repeats)  -window_masker_taxid    Enable WindowMasker filtering using a TaxonomicID  -window_masker_db    Enable WindowMasker filtering using this repeatsdatabase.  -soft_masking    Apply filtering locations as soft masks    Default = `true'  -lcase_masking    Use lower case filtering in query and subjectsequence(s)?  *** Restrict search or results  -gilist    Restrict search of database to list of GI's     * Incompatible with:  negative_gilist,seqidlist, remote, subject,    subject_loc  -seqidlist    Restrict search of database to list ofSeqId's     * Incompatible with:  gilist,negative_gilist, remote, subject,    subject_loc  -negative_gilist    Restrict search of database to everything exceptthe listed GIs     * Incompatible with:  gilist, seqidlist,remote, subject, subject_loc  -entrez_query    Restrict search with the given Entrez query     * Requires:  remote  -db_soft_mask    Filtering algorithm ID to apply to the BLASTdatabase as soft masking     * Incompatible with:  db_hard_mask,subject, subject_loc  -db_hard_mask    Filtering algorithm ID to apply to the BLASTdatabase as hard masking     * Incompatible with:  db_soft_mask,subject, subject_loc  -perc_identity    Percent identity  -culling_limit =0>    If the query range of a hit is enveloped by thatof at least this many    higher-scoring hits, delete the hit     * Incompatible with:  best_hit_overhang,best_hit_score_edge  -best_hit_overhang =0 and =<0.5)>    Best Hit algorithm overhang value (recommendedvalue: 0.1)     * Incompatible with:  culling_limit  -best_hit_score_edge =0 and=<0.5)>    Best Hit algorithm score edge value (recommendedvalue: 0.1)     * Incompatible with:  culling_limit  -max_target_seqs =1>    Maximum number of aligned sequences tokeep     Not applicable for outfmt <= 4    Default = `500'     * Incompatible with:  num_descriptions,num_alignments  *** Discontiguous MegaBLAST options  -template_type    Discontiguous MegaBLAST template type     * Requires:  template_length  -template_length    Discontiguous MegaBLAST template length     * Requires:  template_type  *** Statistical options  -dbsize    Effective length of the database   -searchsp =0>    Effective length of the search space  -max_hsps_per_subject =0>    Override maximum number of HSPs per subject tosave for ungapped searches    (0 means do not override)    Default = `0'  *** Search strategy options  -import_search_strategy    Search strategy to use     * Incompatible with: export_search_strategy  -export_search_strategy    File name to record the search strategyused     * Incompatible with: import_search_strategy  *** Extension options  -xdrop_ungap    X-dropoff value (in bits) for ungappedextensions  -xdrop_gap    X-dropoff value (in bits) for preliminary gappedextensions  -xdrop_gap_final    X-dropoff value (in bits) for final gappedalignment  -no_greedy    Use non-greedy dynamic programmingextension  -min_raw_gapped_score    Minimum raw gapped score to keep an alignment inthe preliminary gapped and    traceback stages  -ungapped    Perform ungapped alignment only?  -window_size =0>    Multiple hits window size, use 0 to specify 1-hitalgorithm  -off_diagonal_range =0>    Number of off-diagonals to search for the 2ndhit, use 0 to turn off    Default = `0'  *** Miscellaneous options  -parse_deflines    Should the query and subject defline(s) beparsed?  -num_threads=1>    Number of threads (CPUs) to use in the BLASTsearch    Default = `1'     * Incompatible with:  remote  -remote    Execute search remotely?     * Incompatible with:  gilist, seqidlist,negative_gilist, subject_loc,    num_threads