See https://www.ncbi.nlm.nih.gov/books/NBK279684/ for a complete list from NCBI
|option||type||default value||description and notes|
BLAST database name.
Query file name.
Location on the query sequence (Format: start-stop)
Output file name
Expect value (E) for saving hits
File with subject sequence(s) to search.
Location on the subject sequence (Format: start-stop).
Show NCBI GIs in report.
Show one-line descriptions for this number of database sequences.
Show alignments for this number of database sequences.
Number of aligned sequences to keep. Use with report formats that do not have separate definition line and alignment sections such as tabular (all outfmt > 4). Not compatible with num_descriptions or num_alignments. Ties are broken by order of sequences in the database.
Maximum number of HSPs (alignments) to keep for any single query-subject pair. The HSPs shown will be the best as judged by expect value. This number should be an integer that is one or greater. If this option is not set, BLAST shows all HSPs meeting the expect value criteria. Setting it to one will show only the best HSP for every query-subject pair
Produce HTML output
Restrict search of database to GI’s listed in this file. Local searches only.
Restrict search of database to everything except the GI’s listed in this file. Local searches only.
Restrict search with the given Entrez query. Remote searches only.
Delete a hit that is enveloped by at least this many higher-scoring hits.
Best Hit algorithm overhang value (recommended value: 0.1)
Best Hit algorithm score edge value (recommended value: 0.1)
Effective size of the database
Effective length of the search space
Search strategy file to read.
Record search strategy to this file.
Parse query and subject bar delimited sequence identifiers (e.g., gi|129295).
Number of threads (CPUs) to use in blast search.
Execute search on NCBI servers?
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 = Seqalign (JSON),
13 = Multiple-file BLAST JSON,
14 = Multiple-file BLAST XML2,
15 = Single-file BLAST JSON,
16 = Single-file BLAST XML2,
17 = Sequence Alignment/Map (SAM),
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
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
sallacc means All subject accessions
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 gap
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 (for all HSPs)
qcovhsp means Query Coverage Per HSP
qcovus is a measure of Query Coverage that counts a position in a subject sequence for this measure only once. The second time the position is aligned to the query is not counted towards this measure.
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'
Values can be 0 or 1.
Value of 0 indicates that BLAST should multi-thread by having each thread work on a part of the database. This is appropriate for a small number of queries and a larger database (e.g., larger than Swissprot). Value 1 indicates that each thread will take a batch of queries and process them independently. This works well for large query sets (10k residues per thread for BLASTP and 2 million bases per thread for BLASTN) and smaller databases (e.g., Swissprot).