Choose a target database
Helianthus annuus XRQ genome assembly v1r1 - genomic sequences - Nucleotide,1531 genome sequences
Helianthus annuus XRQ genome assembly v1r2 - CDS sequences - Nucleotide,52243 cds sequences
Helianthus annuus XRQ genome assembly v1r2 - gene sequences - Nucleotide,58050 gene sequences
Helianthus annuus XRQ genome assembly v1r2 - mRNA sequences - Nucleotide,52243 mrna sequences
Helianthus annuus XRQ genome assembly v1r2 - ncRNA sequences - Nucleotide,5807 ncrna sequences
Helianthus annuus XRQ genome assembly v1r2 - protein sequences - Protein,52243 prot sequences
Helianthus annuus XRQ genome assembly v1r2 - gene upstream sequences 1000 bp - Nucleotide,58019 upstream1000_gene sequences
Helianthus annuus XRQ genome assembly v1r2 - gene upstream sequences 1000 bp - Nucleotide,58019 upstream1000_gene sequences
Helianthus annuus XRQ genome assembly v1r2 - ncRNA upstream sequences 1000 bp - Nucleotide,4930 upstream1000_ncRNA sequences
Helianthus annuus XRQ genome assembly v1r2 - ncRNA upstream sequences 1000 bp - Nucleotide,4930 upstream1000_ncRNA sequences
Helianthus annuus XRQ genome assembly v1r2 - pre_miRNA upstream sequences 1000 bp - Nucleotide,88 upstream1000_pre_miRNA sequences
Helianthus annuus XRQ genome assembly v1r2 - pre_miRNA upstream sequences 1000 bp - Nucleotide,88 upstream1000_pre_miRNA sequences
Helianthus annuus XRQ genome assembly v1r2 - gene upstream sequences 1500 bp - Nucleotide,58019 upstream1500_gene sequences
Helianthus annuus XRQ genome assembly v1r2 - gene upstream sequences 1500 bp - Nucleotide,58019 upstream1500_gene sequences
Helianthus annuus XRQ genome assembly v1r2 - gene upstream sequences 2000 bp - Nucleotide,58019 upstream2000_gene sequences
Helianthus annuus XRQ genome assembly v1r2 - gene upstream sequences 2000 bp - Nucleotide,58019 upstream2000_gene sequences
Helianthus annuus XRQ genome assembly v1r2 - gene upstream sequences 500 bp - Nucleotide,58019 upstream500_gene sequences
Helianthus annuus XRQ genome assembly v1r2 - gene upstream sequences 500 bp - Nucleotide,58019 upstream500_gene sequences
choose a program
blastn: Nucleotide-Nucleotide BLAST
blastp: Protein-Protein BLAST
blastx: Translated Query-Protein Subject BLAST
tblastn: Protein Query-Translated Subject BLAST
tblastx: Translated Query-Translated Subject BLAST
Submit
Reset
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
blastp-short
blastp
deltablast
Word size for wordfinder algorithm (length of best perfect match)
Scoring matrix name (normally BLOSUM62)
PAM70
BLOSUM45
PAM30
BLOSUM80
BLOSUM62
Minimum word score such that the word is added to the BLAST lookup table
Use composition-based statistics
Composition-based statistics as in NAR 29:2994-3005, 2001
no composition-based statistics
Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally
Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties
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
plus
minus
both
General search options
Expectation value (E) threshold for saving hits
Cost to open a gap
Cost to extend a gap
Task to execute
blastn-short
megablast
blastn
rmblastn
dc-megablast
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
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
plus
minus
both
Genetic code to use to translate query
Blepharisma Macronuclear (15)
Alternative Yeast Nuclear (12)
Euplotid Nuclear (10)
Yeast Mitochondrial (3)
Bacteria and Archaea (11)
Echinoderm Mitochondrial (9)
Standard (1)
Mold Mitochondrial; ... (4)
Invertebrate Mitochondrial (5)
Vertebrate Mitochondrial (2)
Flatworm Mitochondrial (14)
Ascidian Mitochondrial (13)
Ciliate Nuclear; ... (6)
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)
PAM30
BLOSUM80
BLOSUM62
PAM70
BLOSUM45
Minimum word score such that the word is added to the BLAST lookup table
Use composition-based statistics
Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties
Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally
no composition-based statistics
Composition-based statistics as in NAR 29:2994-3005, 2001
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
Euplotid Nuclear (10)
Alternative Yeast Nuclear (12)
Blepharisma Macronuclear (15)
Mold Mitochondrial; ... (4)
Standard (1)
Echinoderm Mitochondrial (9)
Bacteria and Archaea (11)
Yeast Mitochondrial (3)
Invertebrate Mitochondrial (5)
Ciliate Nuclear; ... (6)
Ascidian Mitochondrial (13)
Flatworm Mitochondrial (14)
Vertebrate Mitochondrial (2)
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)
BLOSUM62
BLOSUM80
PAM30
BLOSUM45
PAM70
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
both
minus
plus
Genetic code to use to translate query
Ascidian Mitochondrial (13)
Ciliate Nuclear; ... (6)
Flatworm Mitochondrial (14)
Vertebrate Mitochondrial (2)
Invertebrate Mitochondrial (5)
Mold Mitochondrial; ... (4)
Standard (1)
Bacteria and Archaea (11)
Echinoderm Mitochondrial (9)
Yeast Mitochondrial (3)
Euplotid Nuclear (10)
Blepharisma Macronuclear (15)
Alternative Yeast Nuclear (12)
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)
PAM70
BLOSUM45
BLOSUM80
PAM30
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
Mold Mitochondrial; ... (4)
Standard (1)
Yeast Mitochondrial (3)
Bacteria and Archaea (11)
Echinoderm Mitochondrial (9)
Blepharisma Macronuclear (15)
Alternative Yeast Nuclear (12)
Euplotid Nuclear (10)
Ascidian Mitochondrial (13)
Ciliate Nuclear; ... (6)
Vertebrate Mitochondrial (2)
Flatworm Mitochondrial (14)
Invertebrate Mitochondrial (5)
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