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PGDB
a pan-genome database about Pepper
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species
C. rhomboideum
C. annuum
Tool
Blast
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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)
Enter query sequence(s) in the text area.
Or upload your own query FASTA:
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.
Nucleotide
BLAST Databases:
Select a Dataset
capsicum annuum transcripts
capsicum rhomboideum transcripts
Advanced Options
General parameters
Max target sequences:
10
50
100
250
500
1000
5000
10000
20000
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
The length of the seed that initiates an alignment
Scoring parameters
Match/Mismatch Scores:
1,-2
1,-3
1,-4
2,-3
4,-5
1,-1
Reward and penalty for matching and mismatching bases.
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
Cost to create and extend a gap in an alignment.