blastp -help
USAGE
? blastp [-h] [-help] [-import_search_strategy filename]
? ? [-export_search_strategy filename] [-task task_name] [-db database_name]
? ? [-dbsize num_letters] [-gilist filename] [-seqidlist filename]
? ? [-negative_gilist filename] [-negative_seqidlist filename]
? ? [-taxids taxids] [-negative_taxids taxids] [-taxidlist filename]
? ? [-negative_taxidlist filename] [-entrez_query entrez_query]
? ? [-db_soft_mask filtering_algorithm] [-db_hard_mask filtering_algorithm]
? ? [-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]
? ? [-qcov_hsp_perc float_value] [-max_hsps int_value]
? ? [-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]
? ? [-subject_besthit] [-window_size int_value] [-lcase_masking]
? ? [-query_loc range] [-parse_deflines] [-outfmt format] [-show_gis]
? ? [-num_descriptions int_value] [-num_alignments int_value]
? ? [-line_length line_length] [-html] [-max_target_seqs num_sequences]
? ? [-num_threads int_value] [-ungapped] [-remote] [-comp_based_stats compo]
? ? [-use_sw_tback] [-version]
DESCRIPTION
? Protein-Protein BLAST 2.8.1+
OPTIONAL ARGUMENTS
-h
? Print USAGE and DESCRIPTION;? ignore all other parameters
-help
? Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters
-version
? Print version number;? ignore other arguments
*** Input query options
-query <File_In>
? Input file name
? Default = `-'
-query_loc <String>
? Location on the query sequence in 1-based offsets (Format: start-stop)
*** General search options
-task <String, Permissible values: 'blastp' 'blastp-fast' 'blastp-short' >
? Task to execute
? Default = `blastp'
-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:
? ? ? 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
? Default = `2'
*** BLAST-2-Sequences options
-subject <File_In>
? Subject sequence(s) to search
? ? * Incompatible with:? db, gilist, seqidlist, negative_gilist,
? negative_seqidlist, taxids, taxidlist, negative_taxids, negative_taxidlist,
? db_soft_mask, db_hard_mask
-subject_loc <String>
? Location on the subject sequence in 1-based offsets (Format: start-stop)
? ? * Incompatible with:? db, gilist, seqidlist, negative_gilist,
? negative_seqidlist, taxids, taxidlist, negative_taxids, negative_taxidlist,
? db_soft_mask, db_hard_mask, remote
*** Formatting options
-outfmt <String>
? alignment view options:
? ? 0 = Pairwise,
? ? 1 = Query-anchored showing identities,
? ? 2 = Query-anchored no identities,
? ? 3 = Flat query-anchored showing identities,
? ? 4 = Flat query-anchored no identities,
? ? 5 = BLAST XML,
? ? 6 = Tabular,
? ? 7 = Tabular with comment lines,
? ? 8 = Seqalign (Text ASN.1),
? ? 9 = Seqalign (Binary ASN.1),
? ? 10 = Comma-separated values,
? ? 11 = BLAST archive (ASN.1),
? ? 12 = Seqalign (JSON),
? ? 13 = Multiple-file BLAST JSON,
? ? 14 = Multiple-file BLAST XML2,
? ? 15 = Single-file BLAST JSON,
? ? 16 = Single-file BLAST XML2,
? ? 18 = Organism Report
? 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)
? ? ? staxid means Subject Taxonomy ID
? ? ssciname means Subject Scientific Name
? ? scomname means Subject Common Name
? sblastname means Subject Blast Name
? sskingdom means Subject Super Kingdom
? ? staxids means unique Subject Taxonomy ID(s), separated by a ';'
? (in numerical order)
? sscinames means unique Subject Scientific Name(s), separated by a ';'
? scomnames means unique Subject Common Name(s), separated by a ';'
? sblastnames means unique Subject Blast Name(s), separated by a ';'
? (in alphabetical order)
? sskingdoms means unique Subject Super Kingdom(s), separated by a ';'
? (in alphabetical order)
? ? ? stitle means Subject Title
? salltitles means All Subject Title(s), separated by a '<>'
? ? sstrand means Subject Strand
? ? ? qcovs means Query Coverage Per Subject
? ? qcovhsp means Query Coverage Per HSP
? ? ? qcovus means Query Coverage Per Unique Subject (blastn only)
? When not provided, the default value is:
? 'qaccver saccver 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
? Not applicable for outfmt > 4
? 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
-line_length <Integer, >=1>
? Line length for formatting alignments
? Not applicable for outfmt > 4
? Default = `60'
-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 GIs
? ? * Incompatible with:? seqidlist, taxids, taxidlist, negative_gilist,
? negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
? subject_loc
-seqidlist <String>
? Restrict search of database to list of SeqIDs
? ? * Incompatible with:? gilist, taxids, taxidlist, negative_gilist,
? negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
? subject_loc
-negative_gilist <String>
? Restrict search of database to everything except the specified GIs
? ? * Incompatible with:? gilist, seqidlist, taxids, taxidlist,
? negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
? subject_loc
-negative_seqidlist <String>
? Restrict search of database to everything except the specified SeqIDs
? ? * Incompatible with:? gilist, seqidlist, taxids, taxidlist,
? negative_gilist, negative_taxids, negative_taxidlist, remote, subject,
? subject_loc
-taxids <String>
? Restrict search of database to include only the specified taxonomy IDs
? (multiple IDs delimited by ',')
? ? * Incompatible with:? gilist, seqidlist, taxidlist, negative_gilist,
? negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
? subject_loc
-negative_taxids <String>
? Restrict search of database to everything except the specified taxonomy IDs
? (multiple IDs delimited by ',')
? ? * Incompatible with:? gilist, seqidlist, taxids, taxidlist,
? negative_gilist, negative_seqidlist, negative_taxidlist, remote, subject,
? subject_loc
-taxidlist <String>
? Restrict search of database to include only the specified taxonomy IDs
? ? * Incompatible with:? gilist, seqidlist, taxids, negative_gilist,
? negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
? subject_loc
-negative_taxidlist <String>
? Restrict search of database to everything except the specified taxonomy IDs
? ? * Incompatible with:? gilist, seqidlist, taxids, taxidlist,
? negative_gilist, negative_seqidlist, negative_taxids, remote, subject,
? subject_loc
-entrez_query <String>
? Restrict search with the given Entrez query
? ? * Requires:? remote
-db_soft_mask <String>
? Filtering algorithm ID to apply to the BLAST database as soft masking
? ? * Incompatible with:? db_hard_mask, subject, subject_loc
-db_hard_mask <String>
? Filtering algorithm ID to apply to the BLAST database as hard masking
? ? * Incompatible with:? db_soft_mask, subject, subject_loc
-qcov_hsp_perc <Real, 0..100>
? Percent query coverage per hsp
-max_hsps <Integer, >=1>
? Set maximum number of HSPs per subject sequence to save for each query
-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
-subject_besthit
? Turn on best hit per subject sequence
-max_target_seqs <Integer, >=1>
? Maximum number of aligned sequences to keep
? (value of 5 or more is recommended)
? Default = `500'
? ? * Incompatible with:? num_descriptions, num_alignments
*** Statistical options
-dbsize <Int8>
? Effective length of the database
-searchsp <Int8, >=0>
? Effective length of the search space
*** 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
-ungapped
? Perform ungapped alignment only?
*** 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, taxids, taxidlist,
? negative_gilist, negative_seqidlist, negative_taxids, negative_taxidlist,
? subject_loc, num_threads
-use_sw_tback
? Compute locally optimal Smith-Waterman alignments?
