loc
BLAST
-
local NCBI BLAST
Choose Program to Use and Database to Search
Program:
BlastN
BlastP
BlastX
tBlastN
tBlastX
DeltaBlast
PSI-Blast
RPS-Blast
RPS-tBlastN
Database:
Protein Data Bank (PDB)
T.cacao - Criollo - CDS
T.cacao - Criollo - prot
T.cacao - Criollo - genes
T.cacao - Matina - CDS
T.cacao - Matina - prot
T.cacao - Matina - genes
H.umbratica - CDS
H.umbratica - prot
H.umbratica - genes
T.grand - C174 - CDS
T.grand - C174 - prot
T.grand - C174 - genes
T.grand - C1074 - CDS
T.grand - C1074 - prot
T.grand - C1074 - genes
T.grand - C174P - CDS
T.grand - C174P - prot
T.grand - C174P - genes
T.grand - C1074P - CDS
T.grand - C1074P - prot
T.grand - C1074P - genes
T.grand - C174P - genome
T.grand - C1074P - genome
T.grand - C174 - genome
T.grand - C1074 - genome
T.cacao - Matina - genome
T.cacao - Criollo - genome
H.umbratica - genome
Enter sequence below in
FASTA
format (
DEMO
)
Or load it from disk
Output:
Graphical Overview
Plain Text
Algorithm Parameters:
Default
Advanced
Maximum Target Sequences:
0
10
50
100
250
500
Expect Threshold:
0.0001
0.01
1.0
10.0
100.0
1000.0
Word Size:
11
20
24
28
32
48
64
128
256
Match/Mismatch Scores:
Match: 1, Mismatch: -2
Match: 1, Mismatch: -3
Match: 1, Mismatch: -4
Match: 2, Mismatch: -3
Match: 4, Mismatch: -5
Match: 1, Mismatch: -1
Gap Costs:
Linear
Existence: 5, Extension: 2
Existence: 2, Extension: 2
Existence: 1, Extension: 2
Existence: 0, Extension: 2
Existence: 3, Extension: 1
Existence: 2, Extension: 1
Existence: 1, Extension: 1
Filter Low Complexity Regions
Mask for Lookup Table Only
Maximum Target Sequences:
0
10
50
100
250
500
Expect Threshold:
0.0001
0.01
1.0
10.0
100.0
1000.0
Word Size:
6
11
20
24
28
32
48
64
128
256
Matrix:
PAM30
PAM70
PAM250
BLOSUM80
BLOSUM62
BLOSUM45
BLOSUM50
BLOSUM90
Gap Costs:
Existence: 11, Extension: 2
Existence: 10, Extension: 2
Existence: 9, Extension: 2
Existence: 8, Extension: 2
Existence: 7, Extension: 2
Existence: 6, Extension: 2
Existence: 13, Extension: 1
Existence: 12, Extension: 1
Existence: 11, Extension: 1
Existence: 10, Extension: 1
Existence: 9, Extension: 1
Filter Low Complexity Regions
Mask for Lookup Table Only
Maximum Target Sequences:
0
10
50
100
250
500
Expect Threshold:
0.0001
0.01
1.0
10.0
100.0
1000.0
Word Size:
6
11
20
24
28
32
48
64
128
256
Matrix:
PAM30
PAM70
PAM250
BLOSUM80
BLOSUM62
BLOSUM45
BLOSUM50
BLOSUM90
Gap Costs:
Existence: 11, Extension: 2
Existence: 10, Extension: 2
Existence: 9, Extension: 2
Existence: 8, Extension: 2
Existence: 7, Extension: 2
Existence: 6, Extension: 2
Existence: 13, Extension: 1
Existence: 12, Extension: 1
Existence: 11, Extension: 1
Existence: 10, Extension: 1
Existence: 9, Extension: 1
Filter Low Complexity Regions
Mask for Lookup Table Only
Maximum Target Sequences:
0
10
50
100
250
500
Expect Threshold:
0.0001
0.01
1.0
10.0
100.0
1000.0
Word Size:
6
11
20
24
28
32
48
64
128
256
Matrix:
PAM30
PAM70
PAM250
BLOSUM80
BLOSUM62
BLOSUM45
BLOSUM50
BLOSUM90
Gap Costs:
Existence: 11, Extension: 2
Existence: 10, Extension: 2
Existence: 9, Extension: 2
Existence: 8, Extension: 2
Existence: 7, Extension: 2
Existence: 6, Extension: 2
Existence: 13, Extension: 1
Existence: 12, Extension: 1
Existence: 11, Extension: 1
Existence: 10, Extension: 1
Existence: 9, Extension: 1
Filter Low Complexity Regions
Mask for Lookup Table Only
Maximum Target Sequences:
0
10
50
100
250
500
Expect Threshold:
0.0001
0.01
1.0
10.0
100.0
1000.0
Word Size:
2
3
Matrix:
PAM30
PAM70
PAM250
BLOSUM80
BLOSUM62
BLOSUM45
BLOSUM50
BLOSUM90
Strand:
Both
Plus
Minus
Mask for Lookup Table Only
Mask Lower Case Letters
Maximum Target Sequences:
0
10
50
100
250
500
Expect Threshold:
0.0001
0.01
1.0
10.0
100.0
1000.0
Word Size:
2
3
Matrix:
PAM30
PAM70
PAM250
BLOSUM80
BLOSUM62
BLOSUM45
BLOSUM50
BLOSUM90
Gap Costs:
Existence: 11, Extension: 2
Existence: 10, Extension: 2
Existence: 9, Extension: 2
Existence: 8, Extension: 2
Existence: 7, Extension: 2
Existence: 6, Extension: 2
Existence: 13, Extension: 1
Existence: 12, Extension: 1
Existence: 11, Extension: 1
Existence: 10, Extension: 1
Existence: 9, Extension: 1
DELTA-BLAST Threshold:
Pseudocount:
Maximum Target Sequences:
0
10
50
100
250
500
Expect Threshold:
0.0001
0.01
1.0
10.0
100.0
1000.0
Word Size:
2
3
Matrix:
PAM30
PAM70
PAM250
BLOSUM80
BLOSUM62
BLOSUM45
BLOSUM50
BLOSUM90
Gap Costs:
Existence: 11, Extension: 2
Existence: 10, Extension: 2
Existence: 9, Extension: 2
Existence: 8, Extension: 2
Existence: 7, Extension: 2
Existence: 6, Extension: 2
Existence: 13, Extension: 1
Existence: 12, Extension: 1
Existence: 11, Extension: 1
Existence: 10, Extension: 1
Existence: 9, Extension: 1
PSI-BLAST Threshold:
Pseudocount:
Maximum Target Sequences:
0
10
50
100
250
500
Maximum Descriptions:
0
10
50
100
250
500
Expect Threshold:
0.0001
0.01
1.0
10.0
100.0
1000.0
Filter Low Complexity Regions
Mask for Lookup Table Only
Mask Lower Case Letters
Maximum Target Sequences:
0
10
50
100
250
500
Maximum Descriptions:
0
10
50
100
250
500
Expect Threshold:
0.0001
0.01
1.0
10.0
100.0
1000.0
Strand:
Both
Plus
Minus
Filter Low Complexity Regions
Mask for Lookup Table Only
Mask Lower Case Letters