1 /local/gjb_lab/blast+/bin/psiblast -help
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3 psiblast [-h] [-help] [-import_search_strategy filename]
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4 [-export_search_strategy filename] [-db database_name]
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5 [-dbsize num_letters] [-gilist filename] [-negative_gilist filename]
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6 [-entrez_query entrez_query] [-subject subject_input_file]
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7 [-subject_loc range] [-query input_file] [-out output_file]
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8 [-evalue evalue] [-word_size int_value] [-gapopen open_penalty]
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9 [-gapextend extend_penalty] [-xdrop_ungap float_value]
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10 [-xdrop_gap float_value] [-xdrop_gap_final float_value]
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11 [-searchsp int_value] [-seg SEG_options] [-soft_masking soft_masking]
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12 [-matrix matrix_name] [-threshold float_value] [-culling_limit int_value]
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13 [-best_hit_overhang float_value] [-best_hit_score_edge float_value]
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14 [-window_size int_value] [-lcase_masking] [-query_loc range]
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15 [-parse_deflines] [-outfmt format] [-show_gis]
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16 [-num_descriptions int_value] [-num_alignments int_value] [-html]
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17 [-max_target_seqs num_sequences] [-num_threads int_value] [-remote]
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18 [-comp_based_stats compo] [-use_sw_tback] [-gap_trigger float_value]
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19 [-num_iterations int_value] [-out_pssm checkpoint_file]
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20 [-out_ascii_pssm ascii_mtx_file] [-in_msa align_restart]
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21 [-in_pssm psi_chkpt_file] [-pseudocount pseudocount]
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22 [-inclusion_ethresh ethresh] [-phi_pattern file] [-version]
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25 Position-Specific Initiated BLAST 2.2.22+
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29 Print USAGE and DESCRIPTION; ignore other arguments
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31 Print USAGE, DESCRIPTION and ARGUMENTS description; ignore other arguments
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33 Print version number; ignore other arguments
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35 *** Input query options
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39 * Incompatible with: in_msa, in_pssm
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41 Location on the query sequence (Format: start-stop)
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43 *** General search options
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46 * Incompatible with: subject, subject_loc
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51 Expectation value (E) threshold for saving hits
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53 -word_size <Integer, >=2>
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54 Word size for wordfinder algorithm
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57 -gapextend <Integer>
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58 Cost to extend a gap
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61 Default = `BLOSUM62'
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62 -threshold <Real, >=0>
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63 Minimum word score such that the word is added to the BLAST lookup table
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64 -comp_based_stats <String>
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65 Use composition-based statistics for blastp / tblastn:
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66 D or d: default (equivalent to 2)
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67 0 or F or f: no composition-based statistics
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68 1: Composition-based statistics as in NAR 29:2994-3005, 2001
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69 2 or T or t : Composition-based score adjustment as in Bioinformatics
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71 2005, conditioned on sequence properties
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72 3: Composition-based score adjustment as in Bioinformatics 21:902-911,
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73 2005, unconditionally
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74 For programs other than tblastn, must either be absent or be D, F or 0
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77 *** BLAST-2-Sequences options
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79 Subject sequence(s) to search
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80 * Incompatible with: db, gilist, negative_gilist
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81 -subject_loc <String>
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82 Location on the subject sequence (Format: start-stop)
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83 * Incompatible with: db, gilist, negative_gilist, remote
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85 *** Formatting options
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87 alignment view options:
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89 1 = query-anchored showing identities,
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90 2 = query-anchored no identities,
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91 3 = flat query-anchored, show identities,
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92 4 = flat query-anchored, no identities,
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93 5 = XML Blast output,
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95 7 = tabular with comment lines,
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98 10 = Comma-separated values
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100 Options 6, 7, and 10 can be additionally configured to produce
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101 a custom format specified by space delimited format specifiers.
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102 The supported format specifiers are:
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103 qseqid means Query Seq-id
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105 qacc means Query accesion
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106 sseqid means Subject Seq-id
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107 sallseqid means All subject Seq-id(s), separated by a ';'
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108 sgi means Subject GI
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109 sallgi means All subject GIs
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110 sacc means Subject accession
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111 sallacc means All subject accessions
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112 qstart means Start of alignment in query
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113 qend means End of alignment in query
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114 sstart means Start of alignment in subject
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115 send means End of alignment in subject
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116 qseq means Aligned part of query sequence
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117 sseq means Aligned part of subject sequence
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118 evalue means Expect value
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119 bitscore means Bit score
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120 score means Raw score
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121 length means Alignment length
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122 pident means Percentage of identical matches
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123 nident means Number of identical matches
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124 mismatch means Number of mismatches
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125 positive means Number of positive-scoring matches
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126 gapopen means Number of gap openings
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127 gaps means Total number of gaps
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128 ppos means Percentage of positive-scoring matches
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129 frames means Query and subject frames separated by a '/'
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130 qframe means Query frame
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131 sframe means Subject frame
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132 When not provided, the default value is:
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133 'qseqid sseqid pident length mismatch gapopen qstart qend sstart send
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134 evalue bitscore', which is equivalent to the keyword 'std'
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137 Show NCBI GIs in deflines?
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138 -num_descriptions <Integer, >=0>
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139 Number of database sequences to show one-line descriptions for
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141 -num_alignments <Integer, >=0>
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142 Number of database sequences to show alignments for
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145 Produce HTML output?
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147 *** Query filtering options
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149 Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or
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152 -soft_masking <Boolean>
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153 Apply filtering locations as soft masks
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156 Use lower case filtering in query and subject sequence(s)?
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158 *** Restrict search or results
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160 Restrict search of database to list of GI's
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161 * Incompatible with: negative_gilist, remote, subject, subject_loc
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162 -negative_gilist <String>
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163 Restrict search of database to everything except the listed GIs
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164 * Incompatible with: gilist, remote, subject, subject_loc
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165 -entrez_query <String>
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166 Restrict search with the given Entrez query
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168 -culling_limit <Integer, >=0>
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169 If the query range of a hit is enveloped by that of at least this many
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170 higher-scoring hits, delete the hit
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171 * Incompatible with: best_hit_overhang, best_hit_score_edge
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172 -best_hit_overhang <Real, (>=0 and =<0.5)>
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173 Best Hit algorithm overhang value (recommended value: 0.1)
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174 * Incompatible with: culling_limit
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175 -best_hit_score_edge <Real, (>=0 and =<0.5)>
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176 Best Hit algorithm score edge value (recommended value: 0.1)
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177 * Incompatible with: culling_limit
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178 -max_target_seqs <Integer, >=1>
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179 Maximum number of aligned sequences to keep
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181 *** Statistical options
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183 Effective length of the database
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184 -searchsp <Int8, >=0>
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185 Effective length of the search space
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187 *** Search strategy options
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188 -import_search_strategy <File_In>
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189 Search strategy to use
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190 * Incompatible with: export_search_strategy
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191 -export_search_strategy <File_Out>
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192 File name to record the search strategy used
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193 * Incompatible with: import_search_strategy
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195 *** Extension options
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196 -xdrop_ungap <Real>
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197 X-dropoff value (in bits) for ungapped extensions
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199 X-dropoff value (in bits) for preliminary gapped extensions
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200 -xdrop_gap_final <Real>
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201 X-dropoff value (in bits) for final gapped alignment
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202 -window_size <Integer, >=0>
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203 Multiple hits window size, use 0 to specify 1-hit algorithm
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204 -gap_trigger <Real>
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205 Number of bits to trigger gapping
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208 *** Miscellaneous options
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210 Should the query and subject defline(s) be parsed?
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211 -num_threads <Integer, >=1>
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212 Number of threads to use in the BLAST search
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214 * Incompatible with: remote
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216 Execute search remotely?
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217 * Incompatible with: gilist, negative_gilist, subject_loc, num_threads,
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220 Compute locally optimal Smith-Waterman alignments?
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222 *** PSI-BLAST options
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223 -num_iterations <Integer, >=1>
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224 Number of iterations to perform
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226 * Incompatible with: remote
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227 -out_pssm <File_Out>
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228 File name to store checkpoint file
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229 -out_ascii_pssm <File_Out>
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230 File name to store ASCII version of PSSM
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232 File name of multiple sequence alignment to restart PSI-BLAST
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233 * Incompatible with: in_pssm, query
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235 PSI-BLAST checkpoint file
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236 * Incompatible with: in_msa, query, phi_pattern
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238 *** PSSM engine options
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239 -pseudocount <Integer>
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240 Pseudo-count value used when constructing PSSM
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242 -inclusion_ethresh <Real>
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243 E-value inclusion threshold for pairwise alignments
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246 *** PHI-BLAST options
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247 -phi_pattern <File_In>
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248 File name containing pattern to search
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249 * Incompatible with: in_pssm
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