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
Comment