EMBOSS explorer

blast

BLAST search of query sequence(s) against sequence search set (read the manual)

Unshaded fields are optional and can safely be ignored. (hide optional fields)

BLAST program option
Select type of search you want to run
Strand to search
Input section

Query sequence(s). Use one of the following three fields:

  1. To access a sequence from a database, enter the USA here:
  2. To upload a sequence from your local computer, select it here:
  3. To enter the sequence data manually, type here:
Select search set type
Standard nucleic acid search set
Standard protein search set

User defined search set. Use one of the following three fields:

  1. To access a sequence from a database, enter the USA here:
  2. To upload a sequence from your local computer, select it here:
  3. To enter the sequence data manually, type here:
User provided BLAST format databank (you can make one using makeblastdb):
Required section
Word size (default is 11 for blastn and dc_megablast, 28 for megablast, 3 for other search types)
Discontiguous megablast template type
Discontiguous megablast template size
E() value cutoff
Additional section
Make gapped alignments?
Match reward, mismatch penalty, gap penalty, gap length penalty
Match reward, mismatch penalty
Match reward, mismatch penalty, gap length penalty
Amino acid comparison matrix, gap penalty, gap length penalty
Amino acid comparison matrix
Genetic code for translating query sequence(s)
Genetic code for translating databank sequences
Adjustment of scoring scheme according to composition
Advanced section
Filter low complexity segments out of query sequence(s)?
Use soft filtering?
Double hit algorithm?
Multiple hits window size (default is not for blastn or megablast, 40 for other search types)
Effective databank size for statistical calculations
Output section
Keep only n best hits from same region
Alignment format
Show only the n best scoring sequences that satisfy E() cutoff
Show only alignments for the n first sequences (default is 250)
Run section
Email address: If you are submitting a long job and would like to be informed by email when it finishes, enter your email address here.