EMBOSS explorer

blast2seq

Find local alignments between two sequences, using BLAST (read the manual)

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

BLAST program option
Select type of alignment
Strand to search
Input section

Select an input sequence. 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 an input sequence. 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:
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 first (top) sequence
Genetic code for translating second (bottom) sequence
Adjustment of scoring scheme according to composition
Advanced section
Filter low complexity segments out of first (top) sequence?
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
Alignment format
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.