EMBOSS explorer

fastasearch

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

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

fastA package program
Select type of search you want to run
Search also complementary strand?
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 fastA format databank (you can make one using seqret):
Required section
Word (ktup) size (default is 6 for fasta nucleic, 2 for other search types)
E() value cutoff (default is 2.0 for nucleic, 10.0 for protein, 5.0 for fastx/y, 2.0 for tfastx/y)
Additional section
Suboptimal alignments
E2() value cutoff for suboptimal alignments (default is 1/10 of the default value of E())
Nucleotide match reward
Nucleotide mismatch penalty
Amino acid comparison matrix
Adapt amino acid comparison matrix to query sequence length?
Frame shift penalty between codons
Frame shift penalty inside codons
Gap penalty (default is 14 for nucleic, 10 for protein, 12 for mixed)
Gap length penalty (default is 4 for nucleic, 2 for protein, 2 for mixed)
Genetic code for translating sequences
Advanced section
Compute statistics?
Use shuffled databank sequences for statistics
Effective databank size for statistical calculations
Output section
Do not show sequences with E() value lower than f.
Show histogram?
Show only the n best scoring sequences that satisfy E() cutoff
Show only alignments for the n first sequences
Alignment format
Number of residues per line of the alignment
Number of characters for name of databank sequence
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.