Alignments are calculated using the BLOSUM62 scoring matrix.
Gap opening and gap extension penalties are 10 and 1, respectively.
Only alignments with an E-value less than 10-3 are returned.
- You may enter the SwissProt Accession Number of a sequence and leave the NCBI taxonomy ID field blank.
In this case, the sequence belonging to the entered SwissProt Accession Number
will be aligned to all the sequences in SwissProt; alignments of top-scoring sequences will be returned.
- You may also provide a valid NCBI taxonomy identifier in the NCBI taxonomy ID field, while not checking the Include subtree field.
In this case, the entered SwissProt sequence will be aligned to all the SwissProt sequences belonging to the entered NCBI taxonomy identifier.
For example, typing '562' in the NCBI taxonomy ID field filters the output sequences
to contain only alignments of sequences belonging to NCBI taxonomy ID 562 (Escherichia coli).
- In the previous example, a significant number of sequences belonging to Escherichia coli may not be present in the output,
because they have a finer taxonomy classification, thus having different NCBI taxonomy identifiers.
If all the sequences having taxonomy identifiers related to Escherichia Coli are required in the output,
the Include subtree field has to be checked (along with providing the NCBI taxonomy ID of Escherichia coli at the NCBI taxonomy ID field).
Another example would be to filter the outputted alignments to mammalian sequences.
In this case, one may start typing 'Mamma...' in the NCBI taxonomy ID field
to find out that the NCBI taxonomy ID of the node named Mammalia is 40674;
providing this taxonomy identifier while checking the Include subtree field returns the top-scoring alignments
of all the mammalian SwissProt-sequences compared to the entered SwissProt sequence.
Note that in the latter case, not checking the Include subtree field will give no results,
as all sequences in SwissProt have a much finer taxonomy classification, thus none of them has a taxonomy ID 40674.
Gabor Ivan, Daniel Banky, Vince Grolmusz: Fast and Exact Sequence Alignment with the Smith-Waterman Algorithm: The SwissAlign Webserver; Gene Reports, Vol. 4, September 2016, pages 26-28.