blastp options

Input query options

Location on the query sequence in 1-based offsets (Format: start-stop)

General search options

Expectation value (E) threshold for saving hits
Cost to open a gap
Cost to extend a gap
Task to execute
Word size for wordfinder algorithm (length of best perfect match)
Scoring matrix name (normally BLOSUM62)
Minimum word score such that the word is added to the BLAST lookup table
Use composition-based statistics

Formatting options

Show NCBI GIs in deflines
Number of database sequences to show alignments for

Query filtering options

Apply filtering locations as soft masks
Use lower case filtering in query and subject sequence(s)
Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or 'no' to disable)

Restrict search or results

Filtering algorithm ID to apply to the BLAST database as soft masking
Filtering algorithm ID to apply to the BLAST database as hard masking
Percent identity
If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit
Best Hit algorithm overhang value(recommended value : 0.1)
Best Hit algorithm score edge value(recommended value : 0.1)
Maximum number of aligned sequences to keep
Set maximum number of HSPs per subject sequence to save for each query

Statistical options

Effective length of the database
Effective length of the search space

Extension options

X-dropoff value (in bits) for ungapped extensions
Multiple hits window size, use 0 to specify 1-hit algorithm
X-dropoff value (in bits) for preliminary gapped extensions
X-dropoff value (in bits) for final gapped alignment
Perform ungapped alignment only?

Miscellaneous options

Compute locally optimal Smith-Waterman alignments?

blastn options

Input query options

Location on the query sequence in 1-based offsets (Format: start-stop)
Query strand(s) to search against database/subject

General search options

Expectation value (E) threshold for saving hits
Cost to open a gap
Cost to extend a gap
Task to execute
Word size for wordfinder algorithm (length of best perfect match)
Penalty for a nucleotide mismatch
Reward for a nucleotide match

Formatting options

Show NCBI GIs in deflines
Number of database sequences to show alignments for

Query filtering options

Apply filtering locations as soft masks
Use lower case filtering in query and subject sequence(s)
Filter query sequence with DUST(Format :'yes','level window linker', or 'no' to disable)
BLAST database containing filtering elements(i . e . : repeats)
Enable WindowMasker filtering using a Taxonomic ID
Enable WindowMasker filtering using this repeats database .

Restrict search or results

Filtering algorithm ID to apply to the BLAST database as soft masking
Filtering algorithm ID to apply to the BLAST database as hard masking
Percent identity
If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit
Best Hit algorithm overhang value(recommended value : 0.1)
Best Hit algorithm score edge value(recommended value : 0.1)
Maximum number of aligned sequences to keep
Set maximum number of HSPs per subject sequence to save for each query

Statistical options

Effective length of the database
Effective length of the search space

Extension options

X-dropoff value (in bits) for ungapped extensions
Multiple hits window size, use 0 to specify 1-hit algorithm
X-dropoff value (in bits) for preliminary gapped extensions
X-dropoff value (in bits) for final gapped alignment
Use non-greedy dynamic programming extension
Minimum raw gapped score to keep an alignment in the preliminary gapped and traceback stages
Perform ungapped alignment only?
Number of off-diagonals to search for the 2nd hit, use 0 to turn off

Discontiguous MegaBLAST options

Discontiguous MegaBLAST template type
Discontiguous MegaBLAST template length

blastx options

Input query options

Location on the query sequence in 1-based offsets (Format: start-stop)
Query strand(s) to search against database/subject
Genetic code to use to translate query

General search options

Expectation value (E) threshold for saving hits
Cost to open a gap
Cost to extend a gap
Word size for wordfinder algorithm (length of best perfect match)
Length of the largest intron allowed in a translated nucleotide sequence when linking multiple distinct alignments (a negative value disables linking)
Scoring matrix name (normally BLOSUM62)
Minimum word score such that the word is added to the BLAST lookup table
Use composition-based statistics

Formatting options

Show NCBI GIs in deflines
Number of database sequences to show alignments for

Query filtering options

Apply filtering locations as soft masks
Use lower case filtering in query and subject sequence(s)
Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or 'no' to disable)

Restrict search or results

Filtering algorithm ID to apply to the BLAST database as soft masking
Filtering algorithm ID to apply to the BLAST database as hard masking
Percent identity
If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit
Best Hit algorithm overhang value(recommended value : 0.1)
Best Hit algorithm score edge value(recommended value : 0.1)
Maximum number of aligned sequences to keep
Set maximum number of HSPs per subject sequence to save for each query

Statistical options

Effective length of the database
Effective length of the search space

Extension options

X-dropoff value (in bits) for ungapped extensions
Multiple hits window size, use 0 to specify 1-hit algorithm
X-dropoff value (in bits) for preliminary gapped extensions
X-dropoff value (in bits) for final gapped alignment
Perform ungapped alignment only?

Miscellaneous options

Compute locally optimal Smith-Waterman alignments?

tblastn options

Input query options

Location on the query sequence in 1-based offsets (Format: start-stop)

General search options

Expectation value (E) threshold for saving hits
Cost to open a gap
Cost to extend a gap
Word size for wordfinder algorithm (length of best perfect match)
Genetic code to use to translate database/subjects
Length of the largest intron allowed in a translated nucleotide sequence when linking multiple distinct alignments (a negative value disables linking)
Scoring matrix name (normally BLOSUM62)
Minimum word score such that the word is added to the BLAST lookup table

Formatting options

Show NCBI GIs in deflines
Number of database sequences to show alignments for

Query filtering options

Apply filtering locations as soft masks
Use lower case filtering in query and subject sequence(s)
Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or 'no' to disable)

Restrict search or results

Filtering algorithm ID to apply to the BLAST database as soft masking
Filtering algorithm ID to apply to the BLAST database as hard masking
Percent identity
If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit
Best Hit algorithm overhang value(recommended value : 0.1)
Best Hit algorithm score edge value(recommended value : 0.1)
Maximum number of aligned sequences to keep
Set maximum number of HSPs per subject sequence to save for each query

Statistical options

Effective length of the database
Effective length of the search space

Extension options

X-dropoff value (in bits) for ungapped extensions
Multiple hits window size, use 0 to specify 1-hit algorithm

tblastx options

Input query options

Location on the query sequence in 1-based offsets (Format: start-stop)
Query strand(s) to search against database/subject
Genetic code to use to translate query

General search options

Expectation value (E) threshold for saving hits
Cost to open a gap
Cost to extend a gap
Word size for wordfinder algorithm (length of best perfect match)
Scoring matrix name (normally BLOSUM62)
Length of the largest intron allowed in a translated nucleotide sequence when linking multiple distinct alignments (a negative value disables linking)
Minimum word score such that the word is added to the BLAST lookup table
Genetic code to use to translate database/subjects

Formatting options

Show NCBI GIs in deflines
Number of database sequences to show alignments for

Query filtering options

Apply filtering locations as soft masks
Use lower case filtering in query and subject sequence(s)
Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or 'no' to disable)

Restrict search or results

Filtering algorithm ID to apply to the BLAST database as soft masking
Filtering algorithm ID to apply to the BLAST database as hard masking
Percent identity
If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit
Best Hit algorithm overhang value(recommended value : 0.1)
Best Hit algorithm score edge value(recommended value : 0.1)
Maximum number of aligned sequences to keep
Set maximum number of HSPs per subject sequence to save for each query

Statistical options

Effective length of the database
Effective length of the search space

Extension options

X-dropoff value (in bits) for ungapped extensions
Multiple hits window size, use 0 to specify 1-hit algorithm

short options

General search options

Percent identity
Expectation value (E) threshold for saving hits
Cost to open a gap
Cost to extend a gap