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Old 07-13-2013, 05:47 AM   #1
ahmadsam
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Location: best

Join Date: Dec 2011
Posts: 9
Post PSIBlast options

Code:
DESCRIPTION
   Position-Specific Initiated 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 = `-'
    * Incompatible with:  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)
    * Incompatible with:  in_msa, msa_master_idx, ignore_msa_master, in_pssm

 *** General search options
 -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, >=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 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'

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

 *** 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
 -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, negative_gilist, subject_loc,
   num_threads, num_iterations
 -use_sw_tback
   Compute locally optimal Smith-Waterman alignments?

 *** PSI-BLAST options
 -num_iterations <Integer, >=1>
   Number of iterations to perform
   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

 *** 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
ahmadsam is offline   Reply With Quote
Old 10-17-2019, 05:24 PM   #2
fznajar
Member
 
Location: Oklahoma

Join Date: Jan 2012
Posts: 35
Default

Hi all,

has anybody tried to run psiblast with -phi_pattern option? I tried the command with the pattern file as follows:

ID xerD.
PA RX[VL]Q[LM][LM]GH

and I kept getting the following error:
"BLAST engine error: Empty CBlastQueryVector"

Thank you
fznajar is offline   Reply With Quote
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blastp, cog, kog, ortholog, psiblast

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