PSI-BLAST说明书

1、下载
https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/

2、使用案列

 ~/opt/ncbi-blast-2.12.0+/bin/psiblast -query test.fasta -db /home/pub/2018UniRef/uniref50 -out test.out -evalue=1e-3 -outfmt=6   -num_threads=64  -num_iterations=3  -out_pssm=test.pssm  -out_ascii_pssm=test.ascii_pssm -save_pssm_after_last_round

3、使用说明

用法
  psiblast [-h] [-help] [-import_search_strategy filename]
    [-export_search_strategy filename] [-db database_name]
    [-dbsize num_letters] [-gilist filename] [-seqidlist filename]
    [-negative_gilist filename] [-negative_seqidlist filename]
    [-taxids taxids] [-negative_taxids taxids] [-taxidlist filename]
    [-negative_taxidlist filename] [-ipglist filename]
    [-negative_ipglist filename] [-entrez_query entrez_query]
    [-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]
    [-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] [-seg SEG_options] [-soft_masking soft_masking]
    [-matrix matrix_name] [-threshold float_value] [-culling_limit int_value]
    [-best_hit_overhang float_value] [-best_hit_score_edge float_value]
    [-subject_besthit] [-window_size int_value] [-lcase_masking]
    [-query_loc range] [-parse_deflines] [-outfmt format] [-show_gis]
    [-num_descriptions int_value] [-num_alignments int_value]
    [-line_length line_length] [-html] [-sorthits sort_hits]
    [-sorthsps sort_hsps] [-max_target_seqs num_sequences]
    [-num_threads int_value] [-remote] [-comp_based_stats compo]
    [-use_sw_tback] [-gap_trigger float_value] [-num_iterations int_value]
    [-out_pssm checkpoint_file] [-out_ascii_pssm ascii_mtx_file]
    [-save_pssm_after_last_round] [-save_each_pssm] [-in_msa align_restart]
    [-msa_master_idx index] [-ignore_msa_master] [-in_pssm psi_chkpt_file]
    [-pseudocount pseudocount] [-inclusion_ethresh ethresh]
    [-phi_pattern file] [-version]

描述
   Position-Specific Iterated BLAST 2.9.0+

可选参数
 -h
  打印用法与描述；忽略其他参数
 -help
  打印用法，描述与参数；忽略其他参数
 -version
  打印版本号，忽略其他参数

 ***输入查询可选项[ Input query options]
 -query <File_In>
   输入文件名字
   Default = `-'
    * 与这些不兼容:  in_msa, msa_master_idx, ignore_msa_master, in_pssm
 -query_loc <String>
   Location on the query sequence in 1-based offsets (Format: start-stop)
    *与这些不兼容  in_msa, msa_master_idx, ignore_msa_master, in_pssm

 *** General search options
 -db <String>
   BLAST d数据库名称
    * Incompatible with:  subject, subject_loc
 -out <File_Out>
   输出文件名
   Default = `-'
 -evalue <Real>
   保存低于期望阈值结果
   Default = `10'
 -word_size <Integer, >=2>
  设置搜索时字段的大小
 -gapopen <Integer>
   Cost to open a gap
 -gapextend <Integer>
   Cost to extend a gap
 -matrix <String>
  打分矩阵(正常是BLOSUM62)
   Scoring matrix name (normally BLOSUM62)
 -threshold <Real, >=0>
  阈值，低于该分数的搜索结构不保存
   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'

 *** BLAST-2-Sequences options
 -subject <File_In>
   Subject sequence(s) to search
    * Incompatible with:  db, gilist, seqidlist, negative_gilist,
   negative_seqidlist, taxids, taxidlist, negative_taxids, negative_taxidlist,
   ipglist, negative_ipglist
 -subject_loc <String>
   Location on the subject sequence in 1-based offsets (Format: start-stop)
    * Incompatible with:  db, gilist, seqidlist, negative_gilist,
   negative_seqidlist, taxids, taxidlist, negative_taxids, negative_taxidlist,
   ipglist, negative_ipglist, remote

 *** Formatting options
 -outfmt <String>
  输出格式
   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,
    18 = Organism Report
   
   Options 6, 7 and 10 can be additionally configured to produce
   a custom format specified by space delimited format specifiers,
   or by a token specified by the delim keyword.
    E.g.: "17 delim=@ qacc sacc score".
   The delim keyword must appear after the numeric output format
   specification.
   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)
        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'
   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>
    展示最大数据库序列搜索结果
   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?
 -sorthits <Integer, (>=0 and =<4)>
  排序搜索结果
   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

 *** Query filtering options
 -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)?

 *** Restrict search or results#限制搜索或结果
 -gilist <String>
  限制数据库集为给定的ID列表
   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
 -qcov_hsp_perc <Real, 0..100>
   Percent query coverage per hsp
 -max_hsps <Integer, >=1>
    设置HSP每次查询结果的最大数量
   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>
  保存最多的比多结果
   Maximum number of aligned sequences to keep 
   (value of 5 or more is recommended)
   Default = `500'
    * Incompatible with:  num_descriptions, num_alignments

 *** Statistical options统计选项
 -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
 -window_size <Integer, >=0>
   Multiple hits window size, use 0 to specify 1-hit algorithm
 -gap_trigger <Real>
   Number of bits to trigger gapping
   Default = `22'

 *** 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, taxids, taxidlist,
   negative_gilist, negative_seqidlist, negative_taxids, negative_taxidlist,
   subject_loc, num_threads, num_iterations
 -use_sw_tback
   Compute locally optimal Smith-Waterman alignments?

 *** PSI-BLAST options
 -num_iterations <Integer, >=0>
   Number of iterations to perform (0 means run until convergence)
   Default = `1'
    * Incompatible with:  remote
 -out_pssm <File_Out>
   File name to store checkpoint file
 -out_ascii_pssm <File_Out>
   File name to store ASCII version of PSSM
 -save_pssm_after_last_round
    保存最后一侧的PSSM搜索结果
   Save PSSM after the last database search
 -save_each_pssm
   Save PSSM after each iteration (file name is given in -save_pssm or
   -save_ascii_pssm options)

 *** PSSM engine options
 -in_msa <File_In>
   File name of multiple sequence alignment to restart PSI-BLAST
    * Incompatible with:  in_pssm, query, query_loc, phi_pattern
 -msa_master_idx <Integer, >=1>
   Ordinal number (1-based index) of the sequence to use as a master in the
   multiple sequence alignment. If not provided, the first sequence in the
   multiple sequence alignment will be used
    * Requires:  in_msa
    * Incompatible with:  in_pssm, query, query_loc, phi_pattern,
   ignore_msa_master
 -ignore_msa_master
   Ignore the master sequence when creating PSSM
    * Requires:  in_msa
    * Incompatible with:  msa_master_idx, in_pssm, query, query_loc,
   phi_pattern
 -in_pssm <File_In>
   PSI-BLAST checkpoint file
    * Incompatible with:  in_msa, msa_master_idx, ignore_msa_master, query,
   query_loc, phi_pattern
 -pseudocount <Integer>
   Pseudo-count value used when constructing PSSM
   Default = `0'
 -inclusion_ethresh <Real>
   E-value inclusion threshold for pairwise alignments
   Default = `0.002'

 *** PHI-BLAST options
 -phi_pattern <File_In>
   File name containing pattern to search
    * Incompatible with:  in_msa, msa_master_idx, ignore_msa_master, in_pssm