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Vitis_Riparia
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Blast
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Choose a target database
Vitis_Riparia genomic sequences - Nucleotide,174 Riparia.refseq sequences
Vitri_Genes gene - Nucleotide,37239 refseq sequences
Vitri_Genes mRNA - Nucleotide,46963 refseq sequences
Vitri_Genes protein - Protein,46963 refseq 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
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
deltablast
blastp-short
Word size for wordfinder algorithm (length of best perfect match)
Scoring matrix name (normally BLOSUM62)
BLOSUM45
BLOSUM80
BLOSUM62
PAM70
PAM30
Minimum word score such that the word is added to the BLAST lookup table
Use composition-based statistics
no composition-based statistics
Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties
Composition-based statistics as in NAR 29:2994-3005, 2001
Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally
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
Statistical options
Effective length of the database
Effective length of the search space
Override maximum number of HSPs per subject to save for ungapped searches (0 means do not override)
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
minus
plus
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
blastn-short
rmblastn
megablast
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
Statistical options
Effective length of the database
Effective length of the search space
Override maximum number of HSPs per subject to save for ungapped searches (0 means do not override)
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
optimal
coding
coding_and_optimal
Discontiguous MegaBLAST template length
18
16
21
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
both
minus
plus
Genetic code to use to translate query
Ascidian Mitochondrial (13)
Ciliate Nuclear; ... (6)
Vertebrate Mitochondrial (2)
Yeast Mitochondrial (3)
Invertebrate Mitochondrial (5)
Standard (1)
Alternative Yeast Nuclear (12)
Flatworm Mitochondrial (14)
Echinoderm Mitochondrial (9)
Mold Mitochondrial; ... (4)
Blepharisma Macronuclear (15)
Euplotid Nuclear (10)
Bacteria and Archaea (11)
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)
BLOSUM80
BLOSUM45
PAM30
BLOSUM62
PAM70
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
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
no 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
Statistical options
Effective length of the database
Effective length of the search space
Override maximum number of HSPs per subject to save for ungapped searches (0 means do not override)
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
Echinoderm Mitochondrial (9)
Euplotid Nuclear (10)
Blepharisma Macronuclear (15)
Bacteria and Archaea (11)
Mold Mitochondrial; ... (4)
Vertebrate Mitochondrial (2)
Ciliate Nuclear; ... (6)
Ascidian Mitochondrial (13)
Invertebrate Mitochondrial (5)
Standard (1)
Alternative Yeast Nuclear (12)
Flatworm Mitochondrial (14)
Yeast Mitochondrial (3)
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)
BLOSUM80
BLOSUM45
PAM30
BLOSUM62
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
Statistical options
Effective length of the database
Effective length of the search space
Override maximum number of HSPs per subject to save for ungapped searches (0 means do not override)
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
Standard (1)
Invertebrate Mitochondrial (5)
Alternative Yeast Nuclear (12)
Flatworm Mitochondrial (14)
Yeast Mitochondrial (3)
Vertebrate Mitochondrial (2)
Ciliate Nuclear; ... (6)
Ascidian Mitochondrial (13)
Blepharisma Macronuclear (15)
Euplotid Nuclear (10)
Bacteria and Archaea (11)
Mold Mitochondrial; ... (4)
Echinoderm Mitochondrial (9)
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)
BLOSUM80
BLOSUM45
PAM30
PAM70
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)
Bacteria and Archaea (11)
Euplotid Nuclear (10)
Blepharisma Macronuclear (15)
Echinoderm Mitochondrial (9)
Yeast Mitochondrial (3)
Flatworm Mitochondrial (14)
Alternative Yeast Nuclear (12)
Standard (1)
Invertebrate Mitochondrial (5)
Ciliate Nuclear; ... (6)
Ascidian Mitochondrial (13)
Vertebrate Mitochondrial (2)
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
Statistical options
Effective length of the database
Effective length of the search space
Override maximum number of HSPs per subject to save for ungapped searches (0 means do not override)
Extension options
X-dropoff value (in bits) for ungapped extensions
Multiple hits window size, use 0 to specify 1-hit algorithm