Query Sequence
The query sequence must be a amino acid sequence. At present, SALSA will not accept nucleotide query sequences. Entering a nucleotide query sequence will give silly results. The query sequence may be in plain text format, or in FASTA, SWISS-PROT, GenPept or PIR format, in which case a sequence description may be included which will be shown in the output. You may use SRS or Entrez to retrieve your query sequence, and then copy and paste the sequence into the text area. All characters that are not in the set of legal amino acid residue symbols (ABCDEFGHIKLMNPQRSTVWXYZ) in upper or lower case will be removed and ignored. The maximum length of the query sequence is 2000 amino acids.

Sequence Database
You can choose from a wide range of sequence databases, containing both amino acid and nucleotide sequences. In addition to general databases like SWISS-PROT and the non-redundant sequence databases from NCBI, a number of more or less finished genome databases are available. Note that some of the sequence data that is available for searching using this service may be incomplete and may contain errors. In particular, some of the genome sequence data is far from finished and has not been submitted to the general databases (GenBank/EMBL/DDBJ). The non-redundant and EST databases are updated once a week with data from NCBI. The weekly database is updated every night. When searching a nucleotide sequence database, SALSA will translate each database sequence in all six possible frames using the standard genetic code and compare them individually to the amino acid query sequence.

Search Options
The sensitivity, speed and other aspects of the search can be controlled by adjusting the search options. However, for most searches, they can be left at their default values.

• Word size: Selects the number of amino acid residues in the words or tuples used for the initial screening of the sequences to find high-scoring regions. Values: 3 or 4. Default: 3.
• Word score threshold: Determines the minimum score of the pair of initial words or tuples to be considered matching. A low value gives better sensitivity, but takes more time. A high value makes the search faster but less sensitive. Values below 14 are not allowed when searching the large non-redundant nucleotide and EST databases. Values: 11-17. Default: 11.
• Score matrix: Select the amino acid substitution score matrix used to calculate scores. At present, only the BLOSUM62 matrix is available. Values: BLOSUM62. Default BLOSUM62.
• Gap open penalty: The penalty (negative score) given for opening a gap. Used together with the gap extension penalty (see below) to penalize gaps. Not all combinations of gap open and extension penalties are available. Values: 4-11. Default: 10.
• Gap extension penalty: The penalty (negative score) given for extending a gap. Used together with the gap open penalty (see above) to penalize gaps. Values: 1-5. Default: 1.
• Expect: The maximum E-value of a sequence to be reported. The E-value is the expected number of database sequences having at least a certain score. Values: 1-1000. Default: 10.
• Sequences to report: The maximum number of sequences that will be reported. Values: 10, 20, 50, 100, 200, 500, 1000. Default: 1000
• Sequences to align: The maximum number of sequences that will be aligned. Values: 10, 20, 50, 100, 200, 500, 1000. Default: 100
• SW for E<100: Determines if the optimal score (Smith-Waterman) constrained to a band should be calculated for all sequences that have an E-value better than 100. Values: Yes, No. Default: Yes.