This page serves as an interface for homology searches of the clusters and singlets stored in the PEDE database, using your sequence of interest.
Select the EST assembly or cDNA clone set to be used for the BLAST database.
Copy and paste your query sequence for the BLAST search into the text box. Both nucleotide and amino-acid sequences are acceptable, providing that the appropriate search type (BLASTN for nucleotide data; TBLASTN for amino-acid searches) is selected (see below). Nucleotide query sequences must be longer than 11 bp, and amino-acid sequences must contain more than 3 residues. Query sequences must contain fewer than 100,000 characters.
Select the BLAST program appropriate to the submitted sequence. Because the database for the BLAST search is prepared by using nucleotide sequences derived from the assembled results, 2 programs - BLASTN (nucleotide query versus nucleotide database) and TBLASTN (protein query versus nucleotide database) - are available.
Set the upper limit of the expected value of the BLAST search. Results that have the expected value will be displayed. The default value is 10.0; entered values cannot exceed 100.
Define the length of the sequence ("word" or "window") that the BLAST program uses to scan for similarity. If you do not enter any value, the default setting will be used.
Set the number of hit clusters and singlets to be displayed. Values exceeding 500 cannot be entered. The default value is 10; entered values cannot exceed 500.
Set the number of alignment details to be displayed. The default value is 10; entered values cannot exceed 250.
Select the filter if low-complexity sequences are to be masked by using the DUST (BLASTN) or SEG (TBLASTN) program.
Select this feature if the alignment permits the insertion of gaps into the alignment is permitted.
Specify the cost to open a gap. If no value is provided, BLAST runs in the initial setting.
Specify the cost to extend a gap. If no value is provided, BLAST runs in the initial setting.
Specify the reward for a nucleotide match; the default value is 1.
Specify the penalty for a nucleotide mismatch; the default value is -3.