Enter Query Sequence

Enter FASTA sequence

Examples:  #1   #2

Or, upload file

Query subrange

Enter coordinates for a subrange of the query sequence. The BLAST search will apply only to the residues in the range. Sequence coordinates are from 1 to the sequence length.The range includes the residue at the To coordinate.

From 
To 

 

DataBase



Program Selection
Optimize for


 Optimize for Highly similar sequences (megablast)
 Somewhat similar sequences (blastn)
Choose a BLAST algorithm (blastn is default)

Algorithm parameters

General Parameters

Max target sequences

Select the maximum number of aligned sequences to display.

Expect threshold

Expected number of chance matches in a random model.

Word size

The length of the seed that initiates an alignment.


Scoring Parameters

Match/Mismatch Scores

Reward and penalty for matching and mismatching bases.

Gap Costs

Cost to create and extend a gap in an alignment.


Filters and Masking

Filter
 Low complexity

Mask regions of low compositional complexity that may cause spurious or misleading results.

Mask
 Mask for lookup table only

Mask query while producing seeds used to scan database, but not for extensions.


Search database Nucleotide collection (nr/nt) using blastn program

Algorithm parameters

General Parameters

Max target sequences

Select the maximum number of aligned sequences to display.

Expect threshold

Expected number of chance matches in a random model.

Word size

The length of the seed that initiates an alignment.


Scoring Parameters

Match/Mismatch Scores

Reward and penalty for matching and mismatching bases.

Gap Costs

Cost to create and extend a gap in an alignment.


Filters and Masking

Filter
 Low complexity

Mask regions of low compositional complexity that may cause spurious or misleading results.

Mask
 Mask for lookup table only

Mask query while producing seeds used to scan database, but not for extensions.


Search database Nucleotide collection (nr/nt) using megablast program