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Hordeum_vulgare
       
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Choose a target database
HorvuGPTranscriptome__NotEuGeneEvidence_ cds - Nucleotide,152027 cds sequences
HorvuGPTranscriptome__NotEuGeneEvidence_ mrna - Nucleotide,152027 mrna sequences
HorvuGPTranscriptome__NotEuGeneEvidence_ prot - Protein,148092 prot sequences
Annotation_Golden_Promise_v1r1 cds - Nucleotide,71011 cds sequences
Annotation_Golden_Promise_v1r1 gene - Nucleotide,87557 gene sequences
Annotation_Golden_Promise_v1r1 mrna - Nucleotide,71011 mrna sequences
Annotation_Golden_Promise_v1r1 ncrna - Nucleotide,16546 ncrna sequences
Annotation_Golden_Promise_v1r1 prot - Protein,71011 prot sequences
Hordeum_vulgare genomic sequences - Nucleotide,8 vulgare.refseq sequences
Annotation_Golden_Promise_v1r1_Apollo_300620 cds - Nucleotide,70995 cds sequences
Annotation_Golden_Promise_v1r1_Apollo_300620 gene - Nucleotide,87541 gene sequences
Annotation_Golden_Promise_v1r1_Apollo_300620 mrna - Nucleotide,70995 mrna sequences
Annotation_Golden_Promise_v1r1_Apollo_300620 ncrna - Nucleotide,16546 ncrna sequences
Annotation_Golden_Promise_v1r1_Apollo_300620 prot - Protein,70995 prot 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-short
blastp
deltablast
Word size for wordfinder algorithm (length of best perfect match)
Scoring matrix name (normally BLOSUM62)
BLOSUM80
PAM70
PAM30
BLOSUM45
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
Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties
no composition-based statistics
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
both
plus
General search options
Expectation value (E) threshold for saving hits
Cost to open a gap
Cost to extend a gap
Task to execute
megablast
dc-megablast
blastn
blastn-short
rmblastn
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
16
21
18
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
both
minus
Genetic code to use to translate query
Yeast Mitochondrial (3)
Echinoderm Mitochondrial (9)
Ascidian Mitochondrial (13)
Invertebrate Mitochondrial (5)
Alternative Yeast Nuclear (12)
Flatworm Mitochondrial (14)
Standard (1)
Blepharisma Macronuclear (15)
Bacteria and Archaea (11)
Ciliate Nuclear; ... (6)
Mold Mitochondrial; ... (4)
Euplotid Nuclear (10)
Vertebrate Mitochondrial (2)
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)
BLOSUM45
BLOSUM62
BLOSUM80
PAM70
PAM30
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, conditioned on sequence properties
Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally
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
Bacteria and Archaea (11)
Blepharisma Macronuclear (15)
Mold Mitochondrial; ... (4)
Ciliate Nuclear; ... (6)
Euplotid Nuclear (10)
Vertebrate Mitochondrial (2)
Ascidian Mitochondrial (13)
Flatworm Mitochondrial (14)
Standard (1)
Invertebrate Mitochondrial (5)
Alternative Yeast Nuclear (12)
Echinoderm Mitochondrial (9)
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)
PAM70
PAM30
BLOSUM80
BLOSUM62
BLOSUM45
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
Alternative Yeast Nuclear (12)
Invertebrate Mitochondrial (5)
Flatworm Mitochondrial (14)
Standard (1)
Ascidian Mitochondrial (13)
Yeast Mitochondrial (3)
Echinoderm Mitochondrial (9)
Euplotid Nuclear (10)
Vertebrate Mitochondrial (2)
Blepharisma Macronuclear (15)
Ciliate Nuclear; ... (6)
Bacteria and Archaea (11)
Mold Mitochondrial; ... (4)
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)
BLOSUM45
BLOSUM62
BLOSUM80
PAM30
PAM70
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
Vertebrate Mitochondrial (2)
Euplotid Nuclear (10)
Blepharisma Macronuclear (15)
Bacteria and Archaea (11)
Mold Mitochondrial; ... (4)
Ciliate Nuclear; ... (6)
Flatworm Mitochondrial (14)
Standard (1)
Alternative Yeast Nuclear (12)
Invertebrate Mitochondrial (5)
Ascidian Mitochondrial (13)
Yeast Mitochondrial (3)
Echinoderm Mitochondrial (9)
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