blast+中blastp参数详解
2016-11-25 14:20阅读：
查遍网络也没发现有对blastp参数详解的资料，blastn、blastall等资料倒是不少，所以我决定自己动手，把所有的参数解释一遍。
以下是blastp的整体用法概述：
wang@wang-ThinkStation:~/mydata/Accumulibacter/blastp-pro$ 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] [-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] [-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]
[-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 2.2.31+
以下是blastp所有参数的详述：
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
Input file name
Default = `-'
-query_loc
Location on the query sequence in 1-based offsets
(Format: start-stop)
*** General search options
-task
Task to execute
Default = `blastp'
-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 (normally BLOSUM62)
-threshold =0>
Minimum word score such that the word is added to
the BLAST lookup table
-comp_based_stats
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
Subject sequence(s) to search
* Incompatible with: db, gilist,
seqidlist, negative_gilist,
db_soft_mask, db_hard_mask
-subject_loc
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
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,
11 = BLAST archive format (ASN.1),
12 = JSON Seqalign output,
13 = JSON Blast output,
14 = XML2 Blast output
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)
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
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
Not applicable for outfmt > 4
Default = `500'
* Incompatible with:
max_target_seqs
-num_alignments =0>
Number of database sequences to show alignments
for
Default = `250'
* Incompatible with:
max_target_seqs
-line_length =1>
Line length for formatting alignments
Not applicable for outfmt > 4
Default = `60'
-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, seqidlist, remote, subject,
subject_loc
-seqidlist
Restrict search of database to list of
SeqId's
* Incompatible with: gilist,
negative_gilist, remote, subject,
subject_loc
-negative_gilist
Restrict search of database to everything except
the listed GIs
* Incompatible with: gilist,
seqidlist, remote, subject, subject_loc
-entrez_query
Restrict search with the given Entrez query
* Requires: remote
-db_soft_mask
Filtering algorithm ID to apply to the BLAST
database as soft masking
* Incompatible with: db_hard_mask,
subject, subject_loc
-db_hard_mask
Filtering algorithm ID to apply to the BLAST
database as hard masking
* Incompatible with: db_soft_mask,
subject, subject_loc
-qcov_hsp_perc
Percent query coverage per hsp
-max_hsps =1>
Set maximum number of HSPs per subject sequence to
save for each query
-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
Not applicable for outfmt <= 4
Default = `500'
* Incompatible with:
num_descriptions, num_alignments
*** Statistical options
-dbsize
Effective length of the database
-searchsp =0>
Effective length of the search space
-sum_stats
Use sum statistics
*** 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
-ungapped
Perform ungapped alignment only?
*** Miscellaneous options
-parse_deflines
Should the query and subject defline(s) be
parsed?
-num_threads =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?
