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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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Protein to Protein BLAST (blastp)
Request a New BLAST
Enter
Protein
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
protein
BLAST databases listed below.
Protein
BLAST Databases:
Select a Dataset
Capsicum annuum proteins
Capsicum rhomboideum proteins
Advanced Options
General parameters
Max target sequences:
10
50
100
250
500
1000
5000
10000
20000
Select the maximum number of aligned sequences to display
e-value(Expect threshold)
Expected number of chance matches in a random model.
Word size:
3
6
The length of the seed that initiates an alignment
Scoring parameters
Matrix
PAM30
PAM70
PAM250
BLOSUM80
BLOSUM62
BLOSUM45
BLOSUM50
BLOSUM90
Assigns a score for aligning pairs of residues, and determines overall alignment score..
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
Cost to create and extend a gap in an alignment.