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Zymoseptoria_tritici
       
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Choose a target database
JGI_annotation cds - Nucleotide,10931 cds sequences
JGI_annotation mrna - Nucleotide,10931 mrna sequences
JGI_annotation ncrna - Nucleotide,30 ncrna sequences
JGI_annotation prot - Protein,10931 prot sequences
Wageningen_annotation cds - Nucleotide,13157 cds sequences
Wageningen_annotation gene - Nucleotide,13157 gene sequences
Wageningen_annotation mrna - Nucleotide,13157 mrna sequences
Wageningen_annotation prot - Protein,13157 prot sequences
Transposons DNA_transposon - Nucleotide,4265 transposon sequences
Zymoseptoria_tritici genomic sequences - Nucleotide,21 tritici.refseq sequences
MPI_annotation cds - Nucleotide,11839 cds sequences
MPI_annotation gene - Nucleotide,11839 gene sequences
MPI_annotation mrna - Nucleotide,11839 mrna sequences
MPI_annotation prot - Protein,11839 prot sequences
Curtin_annotation cds - Nucleotide,14215 cds sequences
Curtin_annotation gene - Nucleotide,14215 gene sequences
Curtin_annotation mrna - Nucleotide,14215 mrna sequences
Curtin_annotation prot - Protein,14204 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
deltablast
blastp
blastp-short
Word size for wordfinder algorithm (length of best perfect match)
Scoring matrix name (normally BLOSUM62)
BLOSUM62
PAM30
BLOSUM80
PAM70
BLOSUM45
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
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
plus
both
minus
General search options
Expectation value (E) threshold for saving hits
Cost to open a gap
Cost to extend a gap
Task to execute
rmblastn
dc-megablast
blastn-short
blastn
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
coding
coding_and_optimal
optimal
Discontiguous MegaBLAST template length
18
21
16
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
minus
plus
both
Genetic code to use to translate query
Vertebrate Mitochondrial (2)
Blepharisma Macronuclear (15)
Euplotid Nuclear (10)
Yeast Mitochondrial (3)
Alternative Yeast Nuclear (12)
Echinoderm Mitochondrial (9)
Ascidian Mitochondrial (13)
Ciliate Nuclear; ... (6)
Mold Mitochondrial; ... (4)
Standard (1)
Bacteria and Archaea (11)
Flatworm Mitochondrial (14)
Invertebrate Mitochondrial (5)
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)
PAM70
BLOSUM62
PAM30
BLOSUM80
BLOSUM45
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
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
Ciliate Nuclear; ... (6)
Ascidian Mitochondrial (13)
Echinoderm Mitochondrial (9)
Alternative Yeast Nuclear (12)
Flatworm Mitochondrial (14)
Bacteria and Archaea (11)
Invertebrate Mitochondrial (5)
Mold Mitochondrial; ... (4)
Standard (1)
Euplotid Nuclear (10)
Blepharisma Macronuclear (15)
Vertebrate Mitochondrial (2)
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
BLOSUM80
BLOSUM62
PAM30
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
minus
both
plus
Genetic code to use to translate query
Vertebrate Mitochondrial (2)
Blepharisma Macronuclear (15)
Euplotid Nuclear (10)
Yeast Mitochondrial (3)
Alternative Yeast Nuclear (12)
Ascidian Mitochondrial (13)
Echinoderm Mitochondrial (9)
Ciliate Nuclear; ... (6)
Standard (1)
Mold Mitochondrial; ... (4)
Flatworm Mitochondrial (14)
Bacteria and Archaea (11)
Invertebrate Mitochondrial (5)
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)
PAM30
BLOSUM62
BLOSUM80
PAM70
BLOSUM45
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
Flatworm Mitochondrial (14)
Bacteria and Archaea (11)
Invertebrate Mitochondrial (5)
Mold Mitochondrial; ... (4)
Standard (1)
Ascidian Mitochondrial (13)
Ciliate Nuclear; ... (6)
Echinoderm Mitochondrial (9)
Alternative Yeast Nuclear (12)
Yeast Mitochondrial (3)
Euplotid Nuclear (10)
Blepharisma Macronuclear (15)
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