+++ /dev/null
- /local/gjb_lab/blast+/bin/psiblast -help\r
-USAGE\r
- psiblast [-h] [-help] [-import_search_strategy filename]\r
- [-export_search_strategy filename] [-db database_name]\r
- [-dbsize num_letters] [-gilist filename] [-negative_gilist filename]\r
- [-entrez_query entrez_query] [-subject subject_input_file]\r
- [-subject_loc range] [-query input_file] [-out output_file]\r
- [-evalue evalue] [-word_size int_value] [-gapopen open_penalty]\r
- [-gapextend extend_penalty] [-xdrop_ungap float_value]\r
- [-xdrop_gap float_value] [-xdrop_gap_final float_value]\r
- [-searchsp int_value] [-seg SEG_options] [-soft_masking soft_masking]\r
- [-matrix matrix_name] [-threshold float_value] [-culling_limit int_value]\r
- [-best_hit_overhang float_value] [-best_hit_score_edge float_value]\r
- [-window_size int_value] [-lcase_masking] [-query_loc range]\r
- [-parse_deflines] [-outfmt format] [-show_gis]\r
- [-num_descriptions int_value] [-num_alignments int_value] [-html]\r
- [-max_target_seqs num_sequences] [-num_threads int_value] [-remote]\r
- [-comp_based_stats compo] [-use_sw_tback] [-gap_trigger float_value]\r
- [-num_iterations int_value] [-out_pssm checkpoint_file]\r
- [-out_ascii_pssm ascii_mtx_file] [-in_msa align_restart]\r
- [-in_pssm psi_chkpt_file] [-pseudocount pseudocount]\r
- [-inclusion_ethresh ethresh] [-phi_pattern file] [-version]\r
-\r
-DESCRIPTION\r
- Position-Specific Initiated BLAST 2.2.22+\r
-\r
-OPTIONAL ARGUMENTS\r
- -h\r
- Print USAGE and DESCRIPTION; ignore other arguments\r
- -help\r
- Print USAGE, DESCRIPTION and ARGUMENTS description; ignore other arguments\r
- -version\r
- Print version number; ignore other arguments\r
-\r
- *** Input query options\r
- -query <File_In>\r
- Input file name\r
- Default = `-'\r
- * Incompatible with: in_msa, in_pssm\r
- -query_loc <String>\r
- Location on the query sequence (Format: start-stop)\r
-\r
- *** General search options\r
- -db <String>\r
- BLAST database name\r
- * Incompatible with: subject, subject_loc\r
- -out <File_Out>\r
- Output file name\r
- Default = `-'\r
- -evalue <Real>\r
- Expectation value (E) threshold for saving hits\r
- Default = `10'\r
- -word_size <Integer, >=2>\r
- Word size for wordfinder algorithm\r
- -gapopen <Integer>\r
- Cost to open a gap\r
- -gapextend <Integer>\r
- Cost to extend a gap\r
- -matrix <String>\r
- Scoring matrix name\r
- Default = `BLOSUM62'\r
- -threshold <Real, >=0>\r
- Minimum word score such that the word is added to the BLAST lookup table\r
- -comp_based_stats <String>\r
- Use composition-based statistics for blastp / tblastn:\r
- D or d: default (equivalent to 2)\r
- 0 or F or f: no composition-based statistics\r
- 1: Composition-based statistics as in NAR 29:2994-3005, 2001\r
- 2 or T or t : Composition-based score adjustment as in Bioinformatics\r
- 21:902-911,\r
- 2005, conditioned on sequence properties\r
- 3: Composition-based score adjustment as in Bioinformatics 21:902-911,\r
- 2005, unconditionally\r
- For programs other than tblastn, must either be absent or be D, F or 0\r
- Default = `2'\r
-\r
- *** BLAST-2-Sequences options\r
- -subject <File_In>\r
- Subject sequence(s) to search\r
- * Incompatible with: db, gilist, negative_gilist\r
- -subject_loc <String>\r
- Location on the subject sequence (Format: start-stop)\r
- * Incompatible with: db, gilist, negative_gilist, remote\r
-\r
- *** Formatting options\r
- -outfmt <String>\r
- alignment view options:\r
- 0 = pairwise,\r
- 1 = query-anchored showing identities,\r
- 2 = query-anchored no identities,\r
- 3 = flat query-anchored, show identities,\r
- 4 = flat query-anchored, no identities,\r
- 5 = XML Blast output,\r
- 6 = tabular,\r
- 7 = tabular with comment lines,\r
- 8 = Text ASN.1,\r
- 9 = Binary ASN.1\r
- 10 = Comma-separated values\r
-\r
- Options 6, 7, and 10 can be additionally configured to produce\r
- a custom format specified by space delimited format specifiers.\r
- The supported format specifiers are:\r
- qseqid means Query Seq-id\r
- qgi means Query GI\r
- qacc means Query accesion\r
- sseqid means Subject Seq-id\r
- sallseqid means All subject Seq-id(s), separated by a ';'\r
- sgi means Subject GI\r
- sallgi means All subject GIs\r
- sacc means Subject accession\r
- sallacc means All subject accessions\r
- qstart means Start of alignment in query\r
- qend means End of alignment in query\r
- sstart means Start of alignment in subject\r
- send means End of alignment in subject\r
- qseq means Aligned part of query sequence\r
- sseq means Aligned part of subject sequence\r
- evalue means Expect value\r
- bitscore means Bit score\r
- score means Raw score\r
- length means Alignment length\r
- pident means Percentage of identical matches\r
- nident means Number of identical matches\r
- mismatch means Number of mismatches\r
- positive means Number of positive-scoring matches\r
- gapopen means Number of gap openings\r
- gaps means Total number of gaps\r
- ppos means Percentage of positive-scoring matches\r
- frames means Query and subject frames separated by a '/'\r
- qframe means Query frame\r
- sframe means Subject frame\r
- When not provided, the default value is:\r
- 'qseqid sseqid pident length mismatch gapopen qstart qend sstart send\r
- evalue bitscore', which is equivalent to the keyword 'std'\r
- Default = `0'\r
- -show_gis\r
- Show NCBI GIs in deflines?\r
- -num_descriptions <Integer, >=0>\r
- Number of database sequences to show one-line descriptions for\r
- Default = `500'\r
- -num_alignments <Integer, >=0>\r
- Number of database sequences to show alignments for\r
- Default = `250'\r
- -html\r
- Produce HTML output?\r
-\r
- *** Query filtering options\r
- -seg <String>\r
- Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or\r
- 'no' to disable)\r
- Default = `no'\r
- -soft_masking <Boolean>\r
- Apply filtering locations as soft masks\r
- Default = `false'\r
- -lcase_masking\r
- Use lower case filtering in query and subject sequence(s)?\r
-\r
- *** Restrict search or results\r
- -gilist <String>\r
- Restrict search of database to list of GI's\r
- * Incompatible with: negative_gilist, remote, subject, subject_loc\r
- -negative_gilist <String>\r
- Restrict search of database to everything except the listed GIs\r
- * Incompatible with: gilist, remote, subject, subject_loc\r
- -entrez_query <String>\r
- Restrict search with the given Entrez query\r
- * Requires: remote\r
- -culling_limit <Integer, >=0>\r
- If the query range of a hit is enveloped by that of at least this many\r
- higher-scoring hits, delete the hit\r
- * Incompatible with: best_hit_overhang, best_hit_score_edge\r
- -best_hit_overhang <Real, (>=0 and =<0.5)>\r
- Best Hit algorithm overhang value (recommended value: 0.1)\r
- * Incompatible with: culling_limit\r
- -best_hit_score_edge <Real, (>=0 and =<0.5)>\r
- Best Hit algorithm score edge value (recommended value: 0.1)\r
- * Incompatible with: culling_limit\r
- -max_target_seqs <Integer, >=1>\r
- Maximum number of aligned sequences to keep\r
-\r
- *** Statistical options\r
- -dbsize <Int8>\r
- Effective length of the database\r
- -searchsp <Int8, >=0>\r
- Effective length of the search space\r
-\r
- *** Search strategy options\r
- -import_search_strategy <File_In>\r
- Search strategy to use\r
- * Incompatible with: export_search_strategy\r
- -export_search_strategy <File_Out>\r
- File name to record the search strategy used\r
- * Incompatible with: import_search_strategy\r
-\r
- *** Extension options\r
- -xdrop_ungap <Real>\r
- X-dropoff value (in bits) for ungapped extensions\r
- -xdrop_gap <Real>\r
- X-dropoff value (in bits) for preliminary gapped extensions\r
- -xdrop_gap_final <Real>\r
- X-dropoff value (in bits) for final gapped alignment\r
- -window_size <Integer, >=0>\r
- Multiple hits window size, use 0 to specify 1-hit algorithm\r
- -gap_trigger <Real>\r
- Number of bits to trigger gapping\r
- Default = `22'\r
-\r
- *** Miscellaneous options\r
- -parse_deflines\r
- Should the query and subject defline(s) be parsed?\r
- -num_threads <Integer, >=1>\r
- Number of threads to use in the BLAST search\r
- Default = `1'\r
- * Incompatible with: remote\r
- -remote\r
- Execute search remotely?\r
- * Incompatible with: gilist, negative_gilist, subject_loc, num_threads,\r
- num_iterations\r
- -use_sw_tback\r
- Compute locally optimal Smith-Waterman alignments?\r
-\r
- *** PSI-BLAST options\r
- -num_iterations <Integer, >=1>\r
- Number of iterations to perform\r
- Default = `1'\r
- * Incompatible with: remote\r
- -out_pssm <File_Out>\r
- File name to store checkpoint file\r
- -out_ascii_pssm <File_Out>\r
- File name to store ASCII version of PSSM\r
- -in_msa <File_In>\r
- File name of multiple sequence alignment to restart PSI-BLAST\r
- * Incompatible with: in_pssm, query\r
- -in_pssm <File_In>\r
- PSI-BLAST checkpoint file\r
- * Incompatible with: in_msa, query, phi_pattern\r
-\r
- *** PSSM engine options\r
- -pseudocount <Integer>\r
- Pseudo-count value used when constructing PSSM\r
- Default = `0'\r
- -inclusion_ethresh <Real>\r
- E-value inclusion threshold for pairwise alignments\r
- Default = `0.002'\r
-\r
- *** PHI-BLAST options\r
- -phi_pattern <File_In>\r
- File name containing pattern to search\r
- * Incompatible with: in_pssm\r
git://source.jalview.org / jabaws.git / blobdiff