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Tools
BLAST
Nucleotide Query
Nucleotide to Nucleotide BLAST (blastn)
Nucleotide to Nucleotide BLAST (blastn)
Request a New BLAST
Enter
Nucleotide
Query Sequence
Enter one or more queries in the top text box or use the browse button to upload a file from your local disk. The file may contain a single sequence or a list of sequences. In both cases, the data must be in
FASTA format
.
Show an Example Sequence
Enter FASTA sequence(s)
Or upload your own query FASTA:
Upload
The file should be a plain-text FASTA (.fasta, .fna, .fa, .fas) file. In other words, it cannot have formatting as is the case with MS Word (.doc, .docx) or Rich Text Format (.rtf). It cannot be greater than
2MB
in size.
Don't forget to press the Upload button before attempting to submit your BLAST.
Choose Search Target
Choose from one of the
nucleotide
BLAST databases listed below. You can also use the browse button to upload a file from your local disk. The file may contain a single sequence or a list of sequences.
Nucleotide
BLAST Databases:
Select a Dataset
APPV Public Strain Database (updated 05-Apr-2024)
ASFV Public Strain Database (updated 05-Apr-2024)
BV Public Strain Database (updated 05-Apr-2024)
CSFV Public Strain Database (updated 05-Apr-2024)
FMDV Public Strain Database (updated 05-Apr-2024)
PCV1 Public Strain Database (updated 05-Apr-2024)
PCV2 Public Strain Database (updated 05-Apr-2024)
PCV3 Public Strain Database (updated 05-Apr-2024)
PCV4 Public Strain Database (updated 05-Apr-2024)
PDCoV Public Strain Database (updated 05-Apr-2024)
PEDV Public Strain Database (updated 05-Apr-2024)
PPV Public Strain Database (updated 05-Apr-2024)
PRCoV Public Strain Database (updated 05-Apr-2024)
PRRSV-1 Public Strain Database (updated 05-Apr-2024)
PRRSV-2 Public Strain Database (updated 05-Apr-2024)
PRV-A Public Strain Database (updated 05-Apr-2024)
PRV-B Public Strain Database (updated 05-Apr-2024)
PRV-C Public Strain Database (updated 05-Apr-2024)
PSV Public Strain Database (updated 05-Apr-2024)
PTV Public Strain Database (updated 05-Apr-2024)
PsRV Public Strain Database (updated 05-Apr-2024)
SADS-CoV Public Strain Database (updated 05-Apr-2024)
SHEV Public Strain Database (updated 05-Apr-2024)
SVA Public Strain Database (updated 05-Apr-2024)
SVDV Public Strain Database (updated 05-Apr-2024)
TGEV Public Strain Database (updated 05-Apr-2024)
US-SPD Aggregated Public Strain Database (updated 05-Apr-2024)
VSIV Public Strain Database (updated 05-Apr-2024)
VSNJV Public Strain Database (updated 05-Apr-2024)
Or upload your own dataset:
Upload
The file should be a plain-text FASTA (.fasta, .fna, .fa) file. In other words, it cannot have formatting as is the case with MS Word (.doc, .docx) or Rich Text Format (.rtf). It cannot be greater than
2MB
in size.
Don't forget to press the Upload button before attempting to submit your BLAST.
Advanced Options
General parameters
Max target sequences:
10
50
100
250
500
Select the maximum number of unique target sequences per query sequence to show results for. Results returned may not be the highest scoring hits.
More Information
e-Value (Expected Threshold)
Expected number of chance matches in a random model. This number should be give in a decimal format.
More Information
|
Expect value video tutorial
Word size:
7
11
15
16
20
24
28
32
48
64
128
256
Scoring parameters
Match/Mismatch Scores:
1,-2
1,-3
1,-4
2,-3
4,-5
1,-1
Gap Costs:
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
BLAST