Appendix
Commands for BLAST v2.2.28+ (this is not up-to-date)
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]
[-xdrop_ungap float_value] [-xdrop_gap float_value]
[-xdrop_gap_final float_value] [-searchsp int_value]
[-max_hsps_per_subject 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]
[-window_size int_value] [-lcase_masking] [-query_loc range]
[-parse_deflines] [-outfmt format] [-show_gis]
[-num_descriptions int_value] [-num_alignments int_value] [-html]
[-max_target_seqs num_sequences] [-num_threads int_value] [-ungapped]
[-remote] [-comp_based_stats compo] [-use_sw_tback] [-version]
DESCRIPTION
Protein-Protein BLAST 2.2.28+
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-short' 'deltablast' >
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,
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, 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)
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 Subject Taxonomy ID(s), separated by a ';'
sscinames means Subject Scientific Name(s), separated by a ';'
scomnames means Subject Common Name(s), separated by a ';'
sblastnames means Subject Blast Name(s), separated by a ';'
(in alphabetical order)
sskingdoms means Subject Super Kingdom(s), separated by a ';'
(in alphabetical order)
stitle means Subject Title
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