/local/gjb_lab/blast+/bin/psiblast -help USAGE psiblast [-h] [-help] [-import_search_strategy filename] [-export_search_strategy filename] [-db database_name] [-dbsize num_letters] [-gilist filename] [-negative_gilist 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] [-xdrop_ungap float_value] [-xdrop_gap float_value] [-xdrop_gap_final float_value] [-searchsp int_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] [-window_size int_value] [-lcase_masking] [-query_loc range] [-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] [-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] [-in_msa align_restart] [-in_pssm psi_chkpt_file] [-pseudocount pseudocount] [-inclusion_ethresh ethresh] [-phi_pattern file] [-version] DESCRIPTION Position-Specific Initiated BLAST 2.2.22+ 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 Input file name Default = `-' * Incompatible with: in_msa, in_pssm -query_loc Location on the query sequence (Format: start-stop) *** General search options -db BLAST database name * Incompatible with: subject, subject_loc -out Output file name Default = `-' -evalue Expectation value (E) threshold for saving hits Default = `10' -word_size =2> Word size for wordfinder algorithm -gapopen Cost to open a gap -gapextend Cost to extend a gap -matrix Scoring matrix name Default = `BLOSUM62' -threshold =0> Minimum word score such that the word is added to the BLAST lookup table -comp_based_stats 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 Subject sequence(s) to search * Incompatible with: db, gilist, negative_gilist -subject_loc Location on the subject sequence (Format: start-stop) * Incompatible with: db, gilist, negative_gilist, remote *** Formatting options -outfmt 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 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 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 sallacc means All subject accessions 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 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 =0> Number of database sequences to show one-line descriptions for Default = `500' -num_alignments =0> Number of database sequences to show alignments for Default = `250' -html Produce HTML output? *** Query filtering options -seg Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or 'no' to disable) Default = `no' -soft_masking 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 Restrict search of database to list of GI's * Incompatible with: negative_gilist, remote, subject, subject_loc -negative_gilist Restrict search of database to everything except the listed GIs * Incompatible with: gilist, remote, subject, subject_loc -entrez_query Restrict search with the given Entrez query * Requires: remote -culling_limit =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 =0 and =<0.5)> Best Hit algorithm overhang value (recommended value: 0.1) * Incompatible with: culling_limit -best_hit_score_edge =0 and =<0.5)> Best Hit algorithm score edge value (recommended value: 0.1) * Incompatible with: culling_limit -max_target_seqs =1> Maximum number of aligned sequences to keep *** Statistical options -dbsize Effective length of the database -searchsp =0> Effective length of the search space *** Search strategy options -import_search_strategy Search strategy to use * Incompatible with: export_search_strategy -export_search_strategy File name to record the search strategy used * Incompatible with: import_search_strategy *** Extension options -xdrop_ungap X-dropoff value (in bits) for ungapped extensions -xdrop_gap X-dropoff value (in bits) for preliminary gapped extensions -xdrop_gap_final X-dropoff value (in bits) for final gapped alignment -window_size =0> Multiple hits window size, use 0 to specify 1-hit algorithm -gap_trigger Number of bits to trigger gapping Default = `22' *** Miscellaneous options -parse_deflines Should the query and subject defline(s) be parsed? -num_threads =1> Number of threads to use in the BLAST search Default = `1' * Incompatible with: remote -remote Execute search remotely? * Incompatible with: gilist, negative_gilist, subject_loc, num_threads, num_iterations -use_sw_tback Compute locally optimal Smith-Waterman alignments? *** PSI-BLAST options -num_iterations =1> Number of iterations to perform Default = `1' * Incompatible with: remote -out_pssm File name to store checkpoint file -out_ascii_pssm File name to store ASCII version of PSSM -in_msa File name of multiple sequence alignment to restart PSI-BLAST * Incompatible with: in_pssm, query -in_pssm PSI-BLAST checkpoint file * Incompatible with: in_msa, query, phi_pattern *** PSSM engine options -pseudocount Pseudo-count value used when constructing PSSM Default = `0' -inclusion_ethresh E-value inclusion threshold for pairwise alignments Default = `0.002' *** PHI-BLAST options -phi_pattern File name containing pattern to search * Incompatible with: in_pssm