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blastx.php
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blastx.php
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<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>locBLAST - Local NCBI BLAST+ Search</title>
<link href="style.css" rel="stylesheet" type="text/css" />
</head>
<body>
<div class="output">
<h2 style="text-align: center;"><i style="font-size: medium">loc</i><span style="color:blue; font-size: large">BLAST</span> - <span style="font-size: large;">local NCBI BLAST</span></h2>
<hr class="heffect" />
<div style="padding: 0 15px 0 15px;">
<a href="index.php" title="Go Back to Home"><div style="padding: 0 5px 0 0;" id="back"></div></a>
<h4 style="text-align:center; color:blue" id="top">BLASTX Program Description</h4>
<pre>
USAGE
blastx [-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] [-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]
[-sum_stats bool_value] [-max_intron_length length] [-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] [-ungapped] [-lcase_masking] [-query_loc range]
[-strand strand] [-parse_deflines] [-query_gencode int_value]
[-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] [-remote]
[-comp_based_stats compo] [-use_sw_tback] [-version]
DESCRIPTION
Translated Query-Protein Subject BLAST 2.5.0+
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)
-strand <String, `both', `minus', `plus'>
Query strand(s) to search against database/subject
Default = `both'
-query_gencode <Integer, values between: 1-6, 9-16, 21-25>
Genetic code to use to translate query (see user manual for details)
Default = `1'
*** General search options
-task <String, Permissible values: 'blastx' 'blastx-fast' >
Task to execute
Default = `blastx'
-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
-max_intron_length <Integer, >=0>
Length of the largest intron allowed in a translated nucleotide sequence
when linking multiple distinct alignments
Default = `0'
-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,
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,
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:
'qacc sacc 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 = `12 2.2 2.5'
-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
-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
-max_target_seqs <Integer, >=1>
Maximum number of aligned sequences to keep
Not applicable for outfmt <= 4
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
-sum_stats <Boolean>
Use sum statistics
*** 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, negative_gilist, subject_loc,
num_threads
-use_sw_tback
Compute locally optimal Smith-Waterman alignments?
</pre>
</div>
</div>
</body>
</html>