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BLAST
HMMER
CLUSTAL
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BLAST Databases
Tutorial
Organisms
All organisms
All organisms
Nucleotide
Genome Assembly - 114 databases
Transcript - 257 databases
Peptide
Protein - 146 databases
Query Sequence
Enter sequence below in
FASTA
format:
(load from example:
nucleotide
or
peptide
)
Or load it from disk:
Program
blastn
tblastn
tblastx
blastp
blastx
blastn - Nucleotide vs. Nucleotide
General Parameters
Max target sequences
10
50
100
250
500
Expect threshold
Word size
Scoring Parameters
Match score
Mismatch score
Gap opening penalty
Gap extension penalty
Strand
both
plus
minus
Filters and Masking
Low complexity
Mask for lookup table only
General Parameters
Max target sequences
10
50
100
250
500
Expect threshold
Word size
Scoring Parameters
Matrix
PAM30
PAM70
PAM250
BLOSUM90
BLOSUM80
BLOSUM62
BLOSUM50
BLOSUM45
Threshold
Gap opening penalty
Gap extension penalty
Filters and Masking
Low complexity
Mask for lookup table only
General Parameters
Max target sequences
10
50
100
250
500
Expect threshold
Word size
Scoring Parameters
Matrix
PAM30
PAM70
PAM250
BLOSUM90
BLOSUM80
BLOSUM62
BLOSUM50
BLOSUM45
Threshold
Strand
both
plus
minus
Filters and Masking
Low complexity
Mask for lookup table only
General Parameters
Max target sequences
10
50
100
250
500
Expect threshold
Word size
Scoring Parameters
Matrix
PAM30
PAM70
PAM250
BLOSUM90
BLOSUM80
BLOSUM62
BLOSUM50
BLOSUM45
Threshold
Gap opening penalty
Gap extension penalty
Filters and Masking
Low complexity
Mask for lookup table only
General Parameters
Max target sequences
10
50
100
250
500
Expect threshold
Word size
Scoring Parameters
Matrix
PAM30
PAM70
PAM250
BLOSUM90
BLOSUM80
BLOSUM62
BLOSUM50
BLOSUM45
Threshold
Strand
both
plus
minus
Gap opening penalty
Gap extension penalty
Filters and Masking
Low complexity
Mask for lookup table only